VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Nov 27 2019 - 17:19:17 CST

Hello,

The basic problem appears to be that you are still asking for *all* frames to be loaded prior to starting your analysis ("mol addfile 2gbu_18.dcd waitfor all"), so effectively you aren't using bigdcd at all in this instance. You are also asking for an RMSD with respect to an undefined reference (psf files don't have coordinates!) That's why you are still getting out of memory errors (segfaults). To use bigdcd, you'd want to do something like this:

proc rmsd_time { frame } {
   global sel frame0 nf
   $sel move [measure fit $sel $frame0]
   puts "$frame: [measure rmsd $sel $frame0]"
puts $outfile "$frame [measure rmsd $sel $frame0]"
}
source bigdcd.tcl
set outfile [open rmsd_time.dat w];
set mol [mol new 2gbu_wbn.psf type psf waitfor all]
#Load in a pdb so that you have some frames to compare against.
mol addfile 2gbu_wbn.pdb type pdb waitfor all
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbone and noh"]
$frame0 global
$sel global
$outfile global

bigdcd rmsd_time 2gbu_18.dcd
bigdcd_wait
$outfile close
quit

-Josh

On 2019-11-27 09:36:38-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
Hi Everyone,

I’m quite new to the world or VMD/NAMD but have thus far been able to perform 105ns simulations on various protein structures. The major problem however is being able to analyse the trajectories since the memory required is so large. At this point I just want to be able to perform basic analyses using the rmsd and rmsd per residue .tcl scripts found in the ubiquitin tutorial. Despite trying to integrate the dcd scripts with these are am unbale t to get it to work. Errors I have received consist of Segmentation fault (core dumped) and bigdcd and bigdcd_wait not being read. I am trying to run these using ComputeCanada. Here is an example below of the approach I’ve been taking to combine the rmsd.tcl script and commands from the bigdcd scripts (https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/). I have saved the bigdcd.tcl and usually source this before calling the rmsd.tcl. Here is an example of something I’ve tried thus far. Any suggestions much appreciated- many thanks

proc rmsd_time { frame } {
   global sel frame0 nf
   $sel move [measure fit $sel $frame0]
   puts "$frame: [measure rmsd $sel $frame0]"
}
set outfile [open rmsd_time.dat w];
set mol [mol new 2gbu_wbn.psf type psf waitfor all]
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbone and noh"]
mol addfile 2gbu_18.dcd waitfor all
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
    $sel frame $i
    $sel move [measure fit $sel $frame0]
    puts $outfile "[measure rmsd $sel $frame0]"
}
close $outfile
bigdcd rmsd_time
bigdcd_wait
quit

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10