RE: NAMD for inorganics??

From: Ana Celia Araujo Vila Verde (
Date: Thu Nov 23 2006 - 10:39:05 CST

The short answer to your question is yes, provided that the functional forms of your potentials match the ones used by NAMD (you can check the parameter file to find what those are). I'm doing something similar. I did it this way: I produced the psf and pdb files "by hand" (I used tcl scripts to do that) and then altered the parameter file also by hand. Because I produced the pdb and psf files by hand, I didn't have to alter the topology file. I'm away from my office right now but I can send you what I have when I get back in a couple of days (please send me a private reminder if you don't get an email from me by Sunday; it's possible that I'll forget because I'm travelling).



-----Original Message-----
From: on behalf of Vishal Kopardé
Sent: Tue 11/21/2006 4:18 PM
Subject: namd-l: NAMD for inorganics??
Hi all,
If you know the interaction potential of a particular ion say Ti,
which is not included in the topology and parameter file (or you want
to use a particular interaction potential)provided with NAMD, is it
possible to create your own NAMD format parameter and topology file?
Is so, how?
In other words, if I wish to do simulations of Vanadium pent-oxide
nanowires using NAMD (already knowing the forcefield) is it possible??

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