VMD-L Mailing List

From: Trifan, Anda (atrifan2_at_illinois.edu)
Date: Thu Aug 25 2022 - 11:56:11 CDT

Hope this helps:

# Load the system and the trajectory
source ../load_linkers.tcl
cd analysis_full
foreach mol {0 1 2} {

#set up the atom selections
set sel1 [atomselect $mol "name NZ"]
set sel2 [atomselect $mol "name P and resname POPC"]
set outfile [open gofr_pc_first_$mol.dat w]

#calculate g(r)
for { set i 1} {$i < 500 } {incr i 1} {
                set gr [measure gofr $sel1 $sel2 delta .1 rmax 10 usepbc 1 selupdate 1 first 1 last $i step 1]

#set up the outfile and write out the data

                set r [lindex $gr 0]
                set gr2 [lindex $gr 1]
                set igr [lindex $gr 2]

                set m 0
                foreach j $r k $gr2 l $igr {
                   puts $outfile "$j $k $l"
                }
#}
close $outfile
}

#exit vmd
exit

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Date: Thursday, August 25, 2022 at 11:41 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: DisRG Plugin Availability
Hi,

I would like to calculate the radius of gyration over the course of my NAMD simulation. I came across a paper discussing the DisRG plugin which can be used to calculate the radius of gyration. However, the link provided in the paper is broken and I cannot find any other sites with the code for this plugin. Does anyone have a link to the code so that I can install this plugin?

If not, is there a script that can be used? I found a script on the VMD website for a PDB file, but I cannot find one to loop over the trajectory.

Thank you!