VMD-L Mailing List

From: Thomas C Bishop (bishop_at_tulane.edu)
Date: Wed Jun 02 2010 - 09:24:13 CDT

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