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comd.tcl
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comd.tcl
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# Copyright (c) 2010, University of Pittsburgh
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the <organization> nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
package provide comd 1.0
package require solvate
package require autoionize
package require psfgen
package require autopsf
package require pbctools
package require exectool
set COMD_PATH $env(COMD_PATH)
set PACKAGE_PATH "$COMD_PATH"
set PACKAGEPATH "$COMD_PATH"
variable platform $tcl_platform(platform)
switch $platform {
unix {
set TMPDIR "/tmp" ; # or even $::env(TMPDIR), at times.
} macintosh {
set TMPDIR $::env(TRASH_FOLDER) ;# a better place?
} default {
set TMPDIR [pwd]
catch {set TMPDIR $::env(TMP)}
catch {set TMPDIR $::env(TEMP)}
}
}
namespace eval ::comd:: {
namespace export comd
variable version 1.0
variable w
# Variables for system setup
variable molid -1
# input files
variable walker1_pdb
variable walker2_pdb
variable walker1_chid
variable walker2_chid
# Ionization parameters
variable topo_file [list]
variable solvent_padding_x 15
variable solvent_padding_y 15
variable solvent_padding_z 15
# Minimization parameters
variable para_file [list]
variable temperature 298
variable min_length 500
# ANM-MC-Metropolis parameters
variable anm_cutoff ""
variable dev_mag ""
variable accept_para ""
variable max_steps ""
variable step_cutoff ""
# TMD options
variable spring_k 20000
variable tmd_len 10
# Simulation options
variable comd_cycle 100
variable num_cores ""
variable gpus_selected ""
variable gpus_selection1
variable gpus_selection2
variable gpus_present 1
variable python_path ""
variable NAMD_PATH ""
# output options
variable outputdir
variable output_prefix
variable from_commandline 0
variable run_now 1
variable start_dir [pwd]
# Logvew window counter
variable logcount 0
variable lognames [list]
variable titles [list "Prepare System"]
variable interfaces [list "prepare"]
variable which_mode [lindex $titles 0]
}
proc wsplit {string sep} {
set first [string first $sep $string]
if {$first == -1} {
return [list $string]
} else {
set l [string length $sep]
set left [string range $string 0 [expr {$first-1}]]
set right [string range $string [expr {$first+$l}] end]
return [concat [list $left] [wsplit $right $sep]]
}
}
proc comd::Logview {log_file_name} {
variable logcount
variable lognames
set logindex [lsearch $lognames $log_file_name]
set log .somenonsense
if {$logindex > -1} {
set windowname "log$logindex"
set log .$windowname
}
if {[winfo exists $log] == 0} {
if {$logindex > -1} {
lset lognames $logindex "somenonsense"
}
set logindex $logcount
lappend lognames $log_file_name
set windowname "log$logindex"
set log [toplevel ".$windowname"]
wm title $log "Logfile [lindex [file split $log_file_name] end] ($log_file_name)"
wm resizable $log 1 1
incr logcount
text $log.text -bg White -bd 2 \
-yscrollcommand ".$windowname.vscr set"
scrollbar $log.vscr -command ".$windowname.text yview"
pack $log.text -side left -fill both -expand 1
pack $log.vscr -side right -fill y
}
$log.text configure -state normal
#set count 0
#set tabwidth 0
#foreach family [lsort -dictionary [font families]] {
# $log.text tag configure f[incr count] -font [list $family 10]
# $log.text insert end ${family}:\t {} \
# "This is a simple sampler\n" f$count
# set w [font measure [$log.text cget -font] ${family}:]
# if {$w+5 > $tabwidth} {
# set tabwidth [expr {$w+5}]
# $log.text configure -tabs $tabwidth
# }
#}
$log.text delete 1.0 end
set logfile [open $log_file_name "r"]
set line ""
while {[gets $logfile line] != -1} {
$log.text insert end "$line\n"
}
close $logfile
$log.text yview moveto 1
$log.text configure -state disabled
}
proc ::comd::comdgui {} {
variable w
global env
# If already initialized, just turn on
if [winfo exists .comdgui] {
wm deiconify .comdgui
raise .comdgui
return
}
# Initialize window
set w [toplevel .comdgui]
wm title $w "COllective Molecular Dynamics v$::comd::version"
wm resizable $w 0 0
# Set main frame
set mf [frame $w.main_frame]
# VISUALIZE results
# Prepare System and Simulation Files
set mfa [frame $mf.prepare]
# Select input files
set mfaif [labelframe $mfa.input_files -text "Protein structures:" -bd 2]
# Initial PDB
grid [button $mfaif.ini_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The walker1 protein structure should be given in the standard PDB format."}] \
-row 1 -column 0 -sticky w
grid [label $mfaif.ini_label -text "Initial PDB: " -width 21] \
-row 1 -column 1 -sticky w
grid [entry $mfaif.ini_path -width 47 \
-textvariable ::comd::walker1_pdb] \
-row 1 -column 2 -columnspan 6 -sticky ew
grid [button $mfaif.ini_browse -text "Browse" -width 14 -pady 1 -command {
set tempfile [tk_getOpenFile \
-filetypes {{"PDB files" { .pdb .PDB }} {"All files" *}}]
if {![string equal $tempfile ""]} {
set ::comd::walker1_pdb $tempfile
} }] \
-row 1 -column 8 -columnspan 3 -sticky w
# Final PDB
grid [button $mfaif.fin_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The walker2 protein structure should be given in the standard PDB format."}] \
-row 2 -column 0 -sticky w
grid [label $mfaif.fin_label -text "Final PDB: " -width 21] \
-row 2 -column 1 -sticky w
grid [entry $mfaif.fin_path -width 47 \
-textvariable ::comd::walker2_pdb] \
-row 2 -column 2 -columnspan 6 -sticky ew
grid [button $mfaif.fin_browse -text "Browse" -width 14 -pady 1 -command {
set tempfile [tk_getOpenFile \
-filetypes {{"PDB files" { .pdb .PDB }} {"All files" *}}]
if {![string equal $tempfile ""]} {
set ::comd::walker2_pdb $tempfile
} }] \
-row 2 -column 8 -columnspan 3 -sticky w
grid [button $mfaif.inich_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The chain ID for the walker1 and walker2 structure which should be in the previously imported PDB file."}] \
-row 3 -column 0 -sticky w
grid [label $mfaif.inich_label -text "Initial PDB chain ID: " -width 21] \
-row 3 -column 1 -sticky w
grid [entry $mfaif.inich_entry -width 17 \
-textvariable ::comd::walker1_chid] \
-row 3 -column 2 -columnspan 3 -sticky ew
grid [label $mfaif.separatpr_label -width 6] \
-row 3 -column 5 -sticky w
grid [button $mfaif.finch_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The chain ID for the walker1 structure which should be in the previously imported PDB file."}] \
-row 3 -column 6 -sticky w
grid [label $mfaif.finch_label -text "Final PDB chain ID: " -width 21] \
-row 3 -column 7 -sticky w
grid [entry $mfaif.finch_entry -width 17 \
-textvariable ::comd::walker2_chid] \
-row 3 -column 8 -columnspan 3 -sticky ew
pack $mfaif -side top -ipadx 0 -ipady 5 -fill x -expand 1
# Enter ionization options
set mfaio [labelframe $mfa.ionize_options -text "Ionization parameters" -bd 2]
#Solvation box padding and counter ions
grid [button $mfaio.padding_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "This is the half of the walker1 distance between the protein \
and its imaginary copies under periodic boundary conditions. For systems with \
probes, the resulting padding distance will be slightly larger, due to \
constraint of preserving the ratio of 20 water molecules per probe molecule."}] \
-row 0 -column 0 -sticky w
grid [label $mfaio.padding_label -text "Box padding (A): " -width 21] \
-row 0 -column 1 -sticky w
grid [entry $mfaio.padding_entry_x -width 5 \
-textvariable ::comd::solvent_padding_x] \
-row 0 -column 2 -sticky ew
grid [entry $mfaio.padding_entry_y -width 5 \
-textvariable ::comd::solvent_padding_y] \
-row 0 -column 3 -sticky ew
grid [entry $mfaio.padding_entry_z -width 5 \
-textvariable ::comd::solvent_padding_z] \
-row 0 -column 4 -sticky ew
grid [label $mfaio.separatpr_label -width 6] \
-row 1 -column 5 -sticky w
grid [button $mfaio.neutralize_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "By default, counter ions will be added to neutralize a charged \
system. A charged system (if the protein is charged) may be obtained by unchecking this option."}] \
-row 0 -column 6 -sticky w
grid [label $mfaio.neutralize_label -text "Add counter ions: " -width 21] \
-row 0 -column 7 -sticky w
grid [checkbutton $mfaio.neutralize_check -width 1 \
-variable ::comd::neutralize] \
-row 0 -column 8 -sticky e
grid [entry $mfaio.salt_conc_entry -width 13 \
-textvariable ::comd::salt_concentration] \
-row 0 -column 9 -columnspan 2 -sticky w
$mfaio.neutralize_check select
pack $mfaio -side top -ipadx 0 -ipady 5 -fill x -expand 1
#Topology files
grid [button $mfaio.topo_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "Multiple topology files can be specified that will be given to psfgen package of vmd. \
Therefore, from given static structure this will create bonds, angles and various structural elements \
based on topology parameters provided. Suggested file extension is .top but others will be accepted."}] \
-row 1 -column 0 -sticky w
grid [label $mfaio.topo_label -text "Topology files: " -width 21] \
-row 1 -column 1 -sticky w
grid [frame $mfaio.topo_frame] \
-row 1 -rowspan 6 -column 2 -columnspan 6 -sticky w
scrollbar $mfaio.topo_frame.scroll -command "$mfaio.topo_frame.list yview"
listbox $mfaio.topo_frame.list -activestyle dotbox \
-yscroll "$mfaio.topo_frame.scroll set" \
-width 45 -height 6 -setgrid 1 -selectmode browse \
-listvariable ::comd::topo_file
frame $mfaio.topo_frame.buttons
pack $mfaio.topo_frame.list $mfaio.topo_frame.scroll -side left -fill y -expand 1
grid [button $mfaio.topo_add -text "Add" -width 14 -pady 1 \
-command [namespace code {
set tempfiles [tk_getOpenFile -multiple 1 \
-filetypes { {{Topology files} {.top .TOP .rtf .RTF .str .STR}} {{All files} {*}} }]
if {$tempfiles!=""} {
foreach tempfile $tempfiles {
if {[lsearch $::comd::topo_file $tempfile] > -1} {
tk_messageBox -type ok -title "WARNING" \
-message "$tempfile has already been added to the list."
} else {
lappend ::comd::topo_file $tempfile
}
}
}
}]] \
-row 1 -column 8 -columnspan 3 -sticky w
grid [button $mfaio.topo_delete -text "Remove" -width 14 -pady 1 \
-command [namespace code {
foreach i [.comdgui.main_frame.prepare.ionize_options.topo_frame.list curselection] {
.comdgui.main_frame.prepare.ionize_options.topo_frame.list delete $i
} }]] \
-row 2 -column 8 -columnspan 3 -sticky w
# Enter minimization options
set mfamo [labelframe $mfa.minimize_options -text "Minimization parameters" -bd 2]
#Temperature and minimization length parameters
grid [button $mfamo.temperature_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The temperature for molecular dynamics simulation needs to be entered. The units are in Kelvin."}] \
-row 0 -column 0 -sticky w
grid [label $mfamo.temperature_label -text "Temperature (K): " -width 21] \
-row 0 -column 1 -sticky w
grid [entry $mfamo.temperature_entry -width 17 \
-textvariable ::comd::temperature] \
-row 0 -column 2 -columnspan 3 -sticky ew
grid [label $mfamo.separatpr_label -width 6] \
-row 0 -column 5 -sticky w
grid [button $mfamo.length_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "After running targeted molecular dynamics simulations the walker2 structure needs to be equilibrated into a stable state. Longer minimization creates
more stable structures which will guarantee users have a stable targeted molecular dynamics simulation. The units are in ps. "}] \
-row 0 -column 6 -sticky w
grid [label $mfamo.length_label -text "Minimization length (steps): " -width 21] \
-row 0 -column 7 -sticky w
grid [entry $mfamo.length_entry -width 17 \
-textvariable ::comd::min_length] \
-row 0 -column 8 -columnspan 3 -sticky ew
#Parameter files
grid [button $mfamo.para_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "Multiple parameter files can be specified for the force field.
The file should be provided in par or prm format and include necessary parameters required for NAMD."}] \
-row 1 -column 0 -sticky w
grid [label $mfamo.para_label -text "Parameter files: " -width 21] \
-row 1 -column 1 -sticky w
grid [frame $mfamo.para_frame] \
-row 1 -rowspan 6 -column 2 -columnspan 6 -sticky w
scrollbar $mfamo.para_frame.scroll -command "$mfamo.para_frame.list yview"
listbox $mfamo.para_frame.list -activestyle dotbox \
-yscroll "$mfamo.para_frame.scroll set" \
-width 45 -height 6 -setgrid 1 -selectmode browse \
-listvariable ::comd::para_file
frame $mfamo.para_frame.buttons
pack $mfamo.para_frame.list $mfamo.para_frame.scroll \
-side left -fill y -expand 1
grid [button $mfamo.para_add -text "Add" -width 14 -pady 1 \
-command [namespace code {
set tempfiles [tk_getOpenFile -multiple 1 \
-filetypes { {{Parameter files} {.par .PAR .prm .PRM .str .STR}} {{All files} {*}} }]
if {$tempfiles!=""} {
foreach tempfile $tempfiles {
if {[lsearch $::comd::para_file $tempfile] > -1} {
tk_messageBox -type ok -title "WARNING" \
-message "$tempfile has already been added to the list."
} else {
lappend ::comd::para_file $tempfile
}
}
}
}]] \
-row 1 -column 8 -columnspan 3 -sticky w
grid [button $mfamo.para_delete -text "Remove" -width 14 -pady 1 \
-command [namespace code {
foreach i [.comdgui.main_frame.prepare.minimize_options.para_frame.list curselection] {
.comdgui.main_frame.prepare.minimize_options.para_frame.list delete $i
} }]] \
-row 2 -column 8 -columnspan 3 -sticky w
pack $mfamo -side top -ipadx 0 -ipady 5 -fill x -expand 1
set mfamc [labelframe $mfa.anmmc_options -text "ANM-MC-Metropolis options:" -bd 2]
#grid [button $mfamc.anmcut_help -text "?" -width 1 -padx 0 -pady 0 -command {
# tk_messageBox -type ok -title "HELP" \
# -message "In ANM calculations, the cutoff parameter is the maximum distance that two residues are in contact. The units are A. "}] \
# -row 0 -column 0 -sticky w
#grid [label $mfamc.anmc_label -text "ANM cutoff (A): " -width 21] \
# -row 0 -column 1 -sticky w
#grid [entry $mfamc.anmc_field -width 17 \
# -textvariable ::comd::anm_cutoff] \
# -row 0 -column 2 -columnspan 3 -sticky w
grid [button $mfamc.step_cutoffut_help -text "?" -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "To keep structure intact and to avoid having unrealistic \
and very different structures in ANM-MC step, an rmsd threshold is used. Suggested value is 4 A."}] \
-row 0 -column 0 -sticky w
grid [label $mfamc.step_cutoff_label -text "Step cutoff (A):"] \
-row 0 -column 1 -sticky w
grid [entry $mfamc.step_cutoff_field -width 17 \
-textvariable ::comd::step_cutoff] \
-row 0 -column 2 -columnspan 3 -sticky w
grid [label $mfamc.separatpr1_label -width 6] \
-row 0 -column 5 -sticky w
grid [button $mfamc.dev_mag_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The scaling factor used when disturbing the protein structure in ANM-MC steps. Default and suggested value is 0.1 A."}] \
-row 0 -column 6 -sticky w
grid [label $mfamc.dev_mag_label -text "Deviation (A): " -width 21] \
-row 0 -column 7 -sticky w
grid [entry $mfamc.dev_mag_field -width 17 \
-textvariable ::comd::dev_mag] \
-row 0 -column 8 -columnspan 3 -sticky w
grid [button $mfamc.accept_para_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The starting value for the acceptance parameter in ANM-MC steps. Default and suggested value is 0.1."}] \
-row 1 -column 0 -sticky w
grid [label $mfamc.accept_para_label -text "Acceptance ratio: " -width 21] \
-row 1 -column 1 -sticky w
grid [entry $mfamc.accept_para_field -width 17 \
-textvariable ::comd::accept_para] \
-row 1 -column 2 -columnspan 3 -sticky w
grid [label $mfamc.separatpr2_label -width 6] \
-row 1 -column 5 -sticky w
grid [button $mfamc.max_steps_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The maximal number of steps in ANM-MC step. Default and suggested value is 1000000."}] \
-row 1 -column 6 -sticky w
grid [label $mfamc.max_steps_label -text "Max no of ANM steps: " -width 21] \
-row 1 -column 7 -sticky w
grid [entry $mfamc.max_steps_field -width 17 \
-textvariable ::comd::max_steps] \
-row 1 -column 8 -columnspan 3 -sticky w
pack $mfamc -side top -ipadx 0 -ipady 5 -fill x -expand 1
set mfatm [labelframe $mfa.tmd_options -text "TMD options:" -bd 2]
grid [button $mfatm.spring_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "In targeted molecular dynamics simulation, the target potential is harmonic and \
the spring constant term shows the force applied to a given structure to reach the target structure."}] \
-row 0 -column 0 -sticky w
grid [label $mfatm.spring_label -text "Spring constant: " -width 21] \
-row 0 -column 1 -sticky w
grid [entry $mfatm.spring_field -width 17 \
-textvariable ::comd::spring_k] \
-row 0 -column 2 -columnspan 3 -sticky w
grid [label $mfatm.separatpr2_label -width 6] \
-row 0 -column 5 -sticky w
grid [button $mfatm.tmd_len_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The length of targeted molecular dynamics simulations in the units of ps. The length of collective molecular dynamics will change based on the structure and for a structure with 200 residues suggested length is in the order of hundreds."}] \
-row 0 -column 6 -sticky w
grid [label $mfatm.tmd_len_label -text "TMD length (ps): " -width 21] \
-row 0 -column 7 -sticky w
grid [entry $mfatm.tmd_len_field -width 17 \
-textvariable ::comd::tmd_len] \
-row 0 -column 8 -columnspan 3 -sticky w
pack $mfatm -side top -ipadx 0 -ipady 5 -fill x -expand 1
########################################3
set mfaso [labelframe $mfa.simulation_options -text "Simulation options:" -bd 2]
grid [button $mfaso.cmd_cyc_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "Each CoMD cycle consists of minimization, ANM-MC-Metropolis disturbances and targeted molecular dynamics. Please choose the maximum number of cycles performed. Fewer cycles may be run if the starting and walker2 structures for a given cycle are very close."}] \
-row 0 -column 0 -sticky w
grid [label $mfaso.cmd_cyc_label -text "No of coMD cycles: " -width 21] \
-row 0 -column 1 -sticky w
grid [entry $mfaso.cmd_cyc_field -width 17 \
-textvariable ::comd::comd_cycle] \
-row 0 -column 2 -columnspan 3 -sticky w
grid [label $mfaso.separatpr1_label -width 6] \
-row 0 -column 5 -sticky w
grid [button $mfaso.run_now_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "If this is checked the simulations will run as soon as the system is prepared"}] \
-row 0 -column 6 -sticky w
grid [label $mfaso.run_now_label -text "Run now: " -width 21] \
-row 0 -column 7 -sticky w
grid [label $mfaso.separatpr2_label -width 13] \
-row 1 -column 8 -columnspan 2 -sticky w
grid [checkbutton $mfaso.run_now_check -width 1 \
-variable ::comd::run_now] \
-row 0 -column 10 -sticky e
grid [button $mfaso.gpu_id_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The identifiers for the GPUs that will run your TMD simulation separated by commas. NAMD can use one GPU per thread and multiple threads can share GPUs."}] \
-row 1 -column 0 -sticky w
grid [label $mfaso.gpu_id_label -text "GPU IDs: " -width 21] \
-row 1 -column 1 -sticky w
grid [entry $mfaso.gpu_id_field -width 17 \
-textvariable ::comd::gpus_selected] \
-row 1 -column 2 -columnspan 3 -sticky w
grid [label $mfaso.separatpr3_label -width 6] \
-row 1 -column 5 -sticky w
grid [button $mfaso.num_cores_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "The number of physical cores in the cluster or PC that will run your TMD simulation. NAMD is running parallel on CPUs."}] \
-row 1 -column 6 -sticky w
grid [label $mfaso.num_cores_label -text "No of physical cores: " -width 21] \
-row 1 -column 7 -sticky w
grid [entry $mfaso.num_cores -width 17 \
-textvariable ::comd::num_cores] \
-row 1 -column 8 -columnspan 3 -sticky ew
pack $mfaso -side top -ipadx 0 -ipady 5 -fill x -expand 1
########################################4
set mfaoo [labelframe $mfa.output_options -text "Output options:" -bd 2]
grid [button $mfaoo.outdir_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "Output folder, default is current working directory."}] \
-row 0 -column 0 -sticky w
grid [label $mfaoo.outdir_label -text "Output folder: " -width 21] \
-row 0 -column 1 -sticky w
grid [entry $mfaoo.outdir_path -width 47 -textvariable ::comd::outputdir] \
-row 0 -column 2 -columnspan 6 -sticky ew
grid [button $mfaoo.dcd_browse -text "Browse" -width 14 -pady 1 -command {
set tempfile [tk_chooseDirectory]
if {![string equal $tempfile ""]} {
set ::comd::outputdir $tempfile
}}] \
-row 0 -column 8 -columnspan 3 -sticky w
grid [button $mfaoo.prefix_help -text "?" -width 1 -padx 0 -pady 0 -command {
tk_messageBox -type ok -title "HELP" \
-message "All output files and folders will start with this prefix.\
A unique and descriptive prefix choice may allow running multiple simulations in the same folder."}] \
-row 1 -column 0 -sticky w
grid [label $mfaoo.prefix_label -text "Output prefix: " -width 21] \
-row 1 -column 1 -sticky w
grid [entry $mfaoo.prefix_path -width 17 \
-textvariable ::comd::output_prefix] \
-row 1 -column 2 -columnspan 3 -sticky w
grid [label $mfaoo.separator_label -width 6] \
-row 1 -column 5 -sticky w
pack $mfaoo -side top -ipadx 0 -ipady 5 -fill x -expand 1
# Prepare System
button $mfa.button -text "Prepare System" -command ::comd::Prepare_system -bd 3
pack $mfa.button
pack $mfa -side top -padx 0 -pady 0 -fill x -expand 1
pack $mf -side top -padx 0 -pady 0 -fill x -expand 1
return $w
}
proc ::comd::Prepare_system {} {
# WHAT IS NEW?
# 3.1 - Bug fixes and suchlike
# 3.0 - Can now be run from the command line
# 2.1 - Bug fixes, and file checks
# 2.0 - Improved system setup provides lesser number of solvent atoms
# 2.0 - Cleans up intermediate files
# 2.0 - Outputs a log file for troubleshooting, and further intstructions
# 2.0 - NAMD configuration files are prepared for a single or multiple
# simulations
# HOW THE CODE WORKS
# The code will
# (1) solvate the protein, or everything in the PDB/PSF files that you provide
# (2) add counter ions to neutralize the system
# (3) write output files for each simulation
# Setups of multiple simulations differ only at random number seeds.
# This will be sufficient to result in a different trajectory.
variable w
variable pro
if {$::comd::outputdir != ""} {
if {![file isdirectory $::comd::outputdir]} {
if {[catch {file mkdir $::comd::outputdir}]} {
if {[info exists ::comd::from_commandline]} {
error "Could not make output folder: $::comd::outputdir"
} else {
tk_messageBox -type ok -title "ERROR" \
-message "Could not make output folder: $::comd::outputdir"
}
return
}
}
}
if {$::comd::walker1_pdb == "" || $::comd::walker2_pdb == ""} {
tk_messageBox -type ok -title "ERROR" \
-message "Both PDB files must be specified."
return
}
if {$::comd::solvent_padding_z < 4} {
tk_messageBox -type ok -title "ERROR" \
-message "Solvent box padding parameter must be larger than 4 A at least in the z direction."
return
}
if {[string length [string trim $::comd::output_prefix]] == 0} {
tk_messageBox -type ok -title "ERROR" \
-message "Please enter a descriptive name (prefix) for the system."
return
}
if {$::comd::temperature == ""} {
tk_messageBox -type ok -title "ERROR" \
-message "The temperature must be specified."
return
}
if {$::comd::gpus_selected == ""} {
if {[catch {
set output [eval exec "nvidia-smi"]
set records [split $output "\n"]
set j [llength $records]
set k 0
set i 0
set done_header 0
set found_processes 0
set ::comd::gpus_selected [list]
foreach rec $records {
set found_processes [string match *Processes* $rec]
if {$found_processes == 1} {break}
if {$i == 6 && $done_header == 0} {
set done_header 1
set i 0
} elseif {$done_header && $i == 1} {
set fields [split $rec " "]
lappend ::comd::gpus_selected [lindex $fields 3]
} elseif {$done_header && $i == 3} {
set i 0
}
incr i
incr k
}
set ::comd::gpus_selected [lreplace $::comd::gpus_selected [expr {[llength $::comd::gpus_selected]-1 }] [expr {[llength $::comd::gpus_selected]-1 }]]
}]} {
set ::comd::gpus_present 0
} else {
set ::comd::gpus_present 1
}
} else {
set ::comd::gpus_selected [split $::comd::gpus_selected ","]
}
# Divide the GPUs between the two runs if there are two runs and we have an even number of GPUs
if {[expr {$::comd::walker1_pdb}] ne [expr {$::comd::walker2_pdb}]
&& [expr [llength $::comd::gpus_selected] % 2 == 0]
} then {
set ::comd::gpus_selection1 [list]
set ::comd::gpus_selection2 [list]
for {set i 0} {$i < [expr [llength $::comd::gpus_selected]/2]} {incr i} {
lappend ::comd::gpus_selection1 [lindex $::comd::gpus_selected $i]
lappend selection2 [lindex $::comd::gpus_selected [expr {${i} + [llength $::comd::gpus_selected]/2 }]]
}
} else {
if {[expr [llength $::comd::gpus_selected] > 1]} {
set ::comd::gpus_selected [join $::comd::gpus_selected ","]
}
set ::comd::gpus_selection1 $::comd::gpus_selected
set ::comd::gpus_selection2 $::comd::gpus_selected
}
# Linux version
if {$::comd::num_cores == ""} {
if {!([catch {set num_cores [expr {[eval "exec cat /proc/cpuinfo | grep processor | tail -n 1 | awk \"\{ print \\\$3 \}\""] + 1}]}])} {
set ::comd::num_cores $num_cores
}
}
# Mac version
if {$::comd::num_cores == ""} {
if {!([catch {set num_cores [exec sysctl -a | grep machdep.cpu | grep thread_count | awk "{ print \$2}"]}])} {
set ::comd::num_cores $num_cores
}
}
global env
global COMD_PATH
set log_file [open [file join "$::comd::outputdir" "$::comd::output_prefix.log"] w]
puts $log_file "---==## [clock format [clock seconds]] #==---"
puts $log_file "Version: $::comd::version"
puts $log_file "Info: Logging started for setup of $::comd::output_prefix."
puts $log_file "Solvation: Box padding $::comd::solvent_padding_x A in x, $::comd::solvent_padding_y A in y, $::comd::solvent_padding_z A in z."
####### SOLVATION AND IONIZATION OF WALKER 1 PROTEIN STRUCTURE #######
resetpsf
mol delete all
mol new $::comd::walker1_pdb
if {[info exists ::comd::walker1_chid] && ([string trim $::comd::walker1_chid] != "")} {
set pro [atomselect top "not altloc B and not hydrogen and chain $::comd::walker1_chid"]
} else {
set pro [atomselect top "not altloc B and not hydrogen and protein and not resname UNK"]
}
$pro writepdb init.pdb
mol delete all
mol new init.pdb
if {$::comd::topo_file == [list]} {
lappend ::comd::topo_file "$COMD_PATH/top_all36_prot.rtf"
lappend ::comd::topo_file "$COMD_PATH/toppar_water_ions.str"
}
autopsf -mol top -top $::comd::topo_file -prefix pro
solvate pro_formatted_autopsf.psf pro_formatted_autopsf.pdb \
-x $::comd::solvent_padding_x -y $::comd::solvent_padding_y -z $::comd::solvent_padding_z \
+x $::comd::solvent_padding_x +y $::comd::solvent_padding_y +z $::comd::solvent_padding_z -o pro_wb
set totalcharge 0
foreach charge [[atomselect top "all"] get charge] {
set totalcharge [expr $totalcharge + $charge]
}
# number of CL and NA atoms are determined
set nna 0
set ncl 0
puts $log_file "Ionization: Initial PDB System has a total charge of $totalcharge electrons."
if {$totalcharge > 0} {
set ncl [expr round($totalcharge)]
puts $log_file "Ionization: $ncl chloride ions will be added to walker1."
autoionize -psf pro_wb.psf -pdb pro_wb.pdb \
-o [file join $::comd::outputdir "walker1_ionized"] -from 5 -between 5 -nna $nna -ncl $ncl -seg ION
puts $log_file "Ionization: Initial PDB System is ionized to become neutral."
} elseif {$totalcharge < 0} {
set nna [expr -1 * round($totalcharge)]
puts $log_file "Ionization: $nna sodium ions will be added to walker1."
autoionize -psf pro_wb.psf -pdb pro_wb.pdb \
-o [file join $::comd::outputdir "walker1_ionized"] -from 5 -between 5 -nna $nna -ncl $ncl -seg ION
puts $log_file "Ionization: Initial PDB System is ionized to become neutral."
}
mol new init.pdb
set everyone [atomselect top "all"]
set walker1_lims [measure minmax $everyone]
set walker1_cent [measure center $everyone]
set ixmin [lindex $walker1_lims 0 0]
set ixmax [lindex $walker1_lims 1 0]
set iymin [lindex $walker1_lims 0 1]
set iymax [lindex $walker1_lims 1 1]
set izmin [lindex $walker1_lims 0 2]
set izmax [lindex $walker1_lims 1 2]
set ixcen [lindex $walker1_cent 0]
set iycen [lindex $walker1_cent 1]
set izcen [lindex $walker1_cent 2]
set ixlen [expr {$ixmax-$ixmin+16}]
set iylen [expr {$iymax-$iymin+16}]
set izlen [expr {$izmax-$izmin+16}]
if {[expr {$::comd::walker1_pdb}] ne [expr {$::comd::walker2_pdb}]} {
####### SOLVATION AND IONIZATION OF WALKER 2 PROTEIN STRUCTURE #######
resetpsf
mol delete all
mol new $::comd::walker2_pdb
if {[info exists ::comd::walker2_chid] && ([string trim $::comd::walker2_chid] != "")} {
set pro [atomselect top "not altloc B and not hydrogen and chain $::comd::walker2_chid"]
} else {
set pro [atomselect top "not altloc B and not hydrogen and protein and not resname UNK"]
}
$pro writepdb fino.pdb
mol delete all
mol new fino.pdb
autopsf -mol top -top $::comd::topo_file -prefix pro
solvate pro_formatted_autopsf.psf pro_formatted_autopsf.pdb \
-x $::comd::solvent_padding_x -y $::comd::solvent_padding_y -z $::comd::solvent_padding_z \
+x $::comd::solvent_padding_x +y $::comd::solvent_padding_y +z $::comd::solvent_padding_z -o pro_wb
set totalcharge 0
foreach charge [[atomselect top "all"] get charge] {
set totalcharge [expr $totalcharge + $charge]
}
# number of CL and NA atoms are determined
set nna 0
set ncl 0
puts $log_file "Ionization: Final PDB System has a total charge of $totalcharge electrons."
if {$totalcharge > 0} {
set ncl [expr round($totalcharge)]
puts $log_file "Ionization: $ncl chloride ions will be added to walker2."
autoionize -psf pro_wb.psf -pdb pro_wb.pdb \
-o [file join $::comd::outputdir "walker2_ionized"] -from 5 -between 5 -nna $nna -ncl $ncl -seg ION
puts $log_file "Ionization: Final PDB System is ionized to become neutral."
} elseif {$totalcharge < 0} {
set nna [expr -1 * round($totalcharge)]
puts $log_file "Ionization: $nna sodium ions will be added to walker2."
autoionize -psf pro_wb.psf -pdb pro_wb.pdb \
-o [file join $::comd::outputdir "walker2_ionized"] -from 5 -between 5 -nna $nna -ncl $ncl -seg ION
puts $log_file "Ionization: Final PDB System is ionized to become neutral."
}
mol new fino.pdb
set everyone [atomselect top "all"]
set walker2_lims [measure minmax $everyone]
set walker2_cent [measure center $everyone]
set fxmin [lindex $walker2_lims 0 0]
set fxmax [lindex $walker2_lims 1 0]
set fymin [lindex $walker2_lims 0 1]
set fymax [lindex $walker2_lims 1 1]
set fzmin [lindex $walker2_lims 0 2]
set fzmax [lindex $walker2_lims 1 2]
set fxcen [lindex $walker2_cent 0]
set fycen [lindex $walker2_cent 1]
set fzcen [lindex $walker2_cent 2]
set fxlen [expr {$fxmax-$fxmin+16.0}]
set fylen [expr {$fymax-$fymin+16.0}]
set fzlen [expr {$fzmax-$fzmin+16.0}]
}
####### INITIAL MINIMIZATION OF STARTING PROTEIN STRUCTURES #######
puts $log_file "Simulation: NAMD configuration files for minimization written in ${::comd::output_prefix}_walker1_min"
if {[expr {$::comd::walker1_pdb}] ne [expr {$::comd::walker2_pdb}]} {
puts $log_file "and ${::comd::output_prefix}_walker2_min."
}
close $log_file
if {$::comd::para_file == [list]} {
lappend ::comd::para_file "$COMD_PATH/par_all36m_prot.prm"
lappend ::comd::para_file "$COMD_PATH/toppar_water_ions.str"
}
set tcl_file_name [file join "$::comd::outputdir" "$::comd::output_prefix.tcl"]
set tcl_file [open $tcl_file_name w]
puts $tcl_file "#This tcl file will run full collective molecular dynamics simulation with given parameters."
puts $tcl_file "cd $::comd::outputdir"
puts $tcl_file "set sh_filename \"${::comd::output_prefix}_min0.sh\""
puts $tcl_file "set sh_file \[open \$sh_filename w\]"
puts $tcl_file "package require exectool"
if {$::comd::NAMD_PATH == ""} {
puts $tcl_file "set namd2path \[::ExecTool::find \"namd2\"\]"
} else {
puts $tcl_file "set namd2path ${::comd::NAMD_PATH}"
}
if {$::comd::python_path == ""} {
puts $tcl_file "set python_path \[::ExecTool::find \"python\"\]"
} else {
puts $tcl_file "set python_path $::comd::python_path\/python"
}
puts $tcl_file "if {\$namd2path == \"\"} {"
puts $tcl_file "set err_file \[open \"$::comd::output_prefix.log\" a\]"
puts $tcl_file "puts \$err_file \"ERROR: namd2 binary not found\""
puts $tcl_file "exit"
puts $tcl_file "}"
puts $tcl_file "puts \$sh_file \"\\\#\\\!\\\/bin\\\/bash\""
# If there are two different walkers for initial and final structures, divide the CPU cores between them
if {[expr {$::comd::walker1_pdb}] ne [expr {$::comd::walker2_pdb}]} {
set ::comd::num_cores [expr {$::comd::num_cores / 2}]
}
#if {$::comd::gpus_present} {
# set processes_per_run [expr {[llength [wsplit $::comd::gpus_selection1 ","]] + 1}]
#
# if {[info exists ::comd::num_cores]} {
# set remainder [expr {$::comd::num_cores % $processes_per_run}]
# set processes_per_run [expr {$::comd::num_cores - $remainder - $processes_per_run}]
# }
#} else {
# set processes_per_run [expr {$::comd::num_cores - 1}]
#}
puts $tcl_file "puts \$sh_file \"NAMD=\\\"\$namd2path \+idlepoll \\\"\""
# Walker 1 minimization
puts $tcl_file "file mkdir \"${::comd::output_prefix}_walker1_min\""
puts $tcl_file "set namd_file \[open \[file join \"${::comd::output_prefix}_walker1_min\" \"min.conf\"\] w\]"
puts $tcl_file "puts \$namd_file \"coordinates ..\/walker1_ionized.pdb\""
puts $tcl_file "puts \$namd_file \"structure ..\/walker1_ionized.psf\""
puts $tcl_file "puts \$namd_file \"set temperature $::comd::temperature\""
puts $tcl_file "puts \$namd_file \"set outputname walker1_minimized0\""
puts $tcl_file "puts \$namd_file \"set firsttimestep 0\""
puts $tcl_file "puts \$namd_file \"paraTypeCharmm on\""
foreach tempfile $::comd::para_file {
puts $tcl_file "puts \$namd_file \"parameters $tempfile\""
}
puts $tcl_file "puts \$namd_file \"temperature $::comd::temperature\""
puts $tcl_file "puts \$namd_file \"cellBasisVector1 ${ixlen},0,0\""
puts $tcl_file "puts \$namd_file \"cellBasisVector2 0,${iylen},0\""
puts $tcl_file "puts \$namd_file \"cellBasisVector3 0,0,${izlen}\""
puts $tcl_file "puts \$namd_file \"cellOrigin ${ixcen},${iycen},${izcen}\""
puts $tcl_file "puts \$namd_file \"exclude scaled1-4\""
puts $tcl_file "puts \$namd_file \"1-4scaling 1.0\""
puts $tcl_file "puts \$namd_file \"cutoff 12.0\""
puts $tcl_file "puts \$namd_file \"timestep 1.0\""
puts $tcl_file "puts \$namd_file \"switching on\""
puts $tcl_file "puts \$namd_file \"switchdist 10.0\""
puts $tcl_file "puts \$namd_file \"pairlistdist 13.5\""
puts $tcl_file "puts \$namd_file \"rigidBonds none\""
puts $tcl_file "puts \$namd_file \"nonbondedFreq 1\""
puts $tcl_file "puts \$namd_file \"fullElectFrequency 1\""
puts $tcl_file "puts \$namd_file \"stepspercycle 5\""
puts $tcl_file "puts \$namd_file \"langevin on\""
puts $tcl_file "puts \$namd_file \"langevinDamping 5\""
puts $tcl_file "puts \$namd_file \"langevinTemp \\\$temperature\""
puts $tcl_file "puts \$namd_file \"langevinHydrogen on\""
puts $tcl_file "puts \$namd_file \"outputname \\\$outputname\""
puts $tcl_file "puts \$namd_file \"outputEnergies $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"outputPressure $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"restartfreq $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"dcdfreq $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"xstfreq $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"twoAwayX yes\""
puts $tcl_file "puts \$namd_file \"twoAwayY yes\""
puts $tcl_file "puts \$namd_file \"twoAwayZ yes\""
puts $tcl_file "puts \$namd_file \"minimize $::comd::min_length\""
puts $tcl_file "puts \$namd_file \"reinitvels \\\$temperature\""
puts $tcl_file "close \$namd_file"
puts $tcl_file "puts \$sh_file \"cd ${::comd::output_prefix}_walker1_min\""
puts $tcl_file "puts \$sh_file \"\\\$NAMD \+devices $::comd::gpus_selection1 \+ppn $::comd::num_cores min.conf > min0.log \\|\\| \\\$NAMD \+ppn $::comd::num_cores min.conf > min0.log \&\""
puts $tcl_file "puts \$sh_file \"cd ..\""
if {[expr {$::comd::walker1_pdb}] ne [expr {$::comd::walker2_pdb}]} {
# Walker 2 minimization
puts $tcl_file "file mkdir \"${::comd::output_prefix}_walker2_min\""
puts $tcl_file "set namd_file \[open \[file join \"${::comd::output_prefix}_walker2_min\" \"min.conf\"\] w\]"
puts $tcl_file "puts \$namd_file \"coordinates ..\/walker2_ionized.pdb\""
puts $tcl_file "puts \$namd_file \"structure ..\/walker2_ionized.psf\""
puts $tcl_file "puts \$namd_file \"set temperature $::comd::temperature\""
puts $tcl_file "puts \$namd_file \"set outputname walker2_minimized0\""
puts $tcl_file "puts \$namd_file \"set firsttimestep 0\""
puts $tcl_file "puts \$namd_file \"paraTypeCharmm on\""
foreach tempfile $::comd::para_file {
puts $tcl_file "puts \$namd_file \"parameters $tempfile\""
}
puts $tcl_file "puts \$namd_file \"temperature $::comd::temperature\""