VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Jun 04 2016 - 20:58:06 CDT

Hi Grant,
All that namdenergy is really doing is writing a specific run script for namd. If you try it with the debug option on, you can find and edit that run script in your working directory, and should be able to make it skip frames in the input dcd or do whatever else you want. I suspect it will make more sense when you look at that file, but let me know if you still have questions.
Best,
Peter

> On Jun 3, 2016, at 4:55 PM, Grant Schauer <grantschauer_at_gmail.com> wrote:
>
> Hi all,
>
> I tried to run namdenergy on a very large trajectory with bigdcd (see below), but it seems to be just looping over the same first two frames on repeat, which maybe makes some sense because namdenergy assumes I start at the first frame and I can't pass $frame to it.
>
> Is there a workaround for this? Alternatively, is there a way for namdenergy to handle large dcds frame-by-frame?
>
> Any help appreciated, thanks
> Grant
>
>
> source bigdcd.tcl
> package require namdenergy
>
> set mol [mol new ./molecule.psf type psf waitfor all]
>
> mol addfile ./molecule.pdb type pdb waitfor all
> set sel1 [atomselect top protein]
> set sel2 [atomselect top nucleic]
>
> proc energies {frame} {
> global mol sel1 sel2 out
>
> namdenergy -nonb -vdw -elec -sel $sel1 $sel2 -ofile out.dat -par par_all27_prot_na.prm -par
> }
>
> bigdcd energies dcd ./giant_dcd.dcd
> bigdcd_wait
>
> quit