VMD-L Mailing List
From: Thomas C Bishop (bishop_at_tulane.edu)
Date: Wed Jun 02 2010 - 09:24:13 CDT
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- In reply to: Philip Peartree: "RMSD Trajectory Tool"
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I use something like the following rms.vmd script
and then load vmd as folllows
vmd -parm7 sys.parm -dcd sys.dcd -e rms.vmd
or
vmd -psf sys.psf -dcd sys.dcd -e rms.vmd
to calculate an rms.dat file
************** rms.vmd *************
### TcB_at_Tulane 2010
### bishop_at_tulane.edu
proc rmsd_v_time { mol sel fn } {
# use frame 0 for the reference
set fit [atomselect $mol $sel frame 0]
set comp [atomselect $mol $sel frame 0]
set num_steps [molinfo $mol get numframes]
set fp [open $fn w ]
for {set frame 0} {$frame < $num_steps} {incr frame} {
# get the correct frame
$comp frame $frame
set rms [expr [measure rmsd $comp $fit] ]
puts $fp " $frame $rms "
}
close $fp
}
rmsd_v_time [molinfo top] "all" "rmsd.dat"
quit
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