VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Wed Jan 15 2020 - 23:08:49 CST

A similar question was posted earlier and I did not find any link for the
answers in the NAMD mailing list, So I am copying the answer here

*Credits*:

Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>

Can't you do something like this in your interaction.namd script?

# First frame saved was frame 1000.
set ts 0
foreach dcdfile [list file1.dcd file2.dcd file3.dcd] {
coorfile open dcd $dcdfile.dcd
# Read all frames until nonzero is returned.
while { ![coorfile read] } {
# Set firstTimestep so our energy output has the correct TS.
firstTimestep $ts
# Compute energies and forces, but don’t try to move the atoms.
run 0
incr ts 1
}
coorfile close
}

Thank you

On Thu, Jan 16, 2020 at 1:18 AM Ackad, Edward <eackad_at_siue.edu> wrote:

> Hi all,
> I'm trying to write a python script with minimal dependencies and that
> uses namdEneriy to calculate the energy of a dcd file. Is there a better
> way than externally calling vmd to load the psf+dcd and call namdEnergy
> from within vmd?
>
> Thanks!
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*