Re: How to create multiple molecules using psfgen

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed May 16 2018 - 07:06:12 CDT

You can iterate every psfgen command using a Tcl "for" loop.

On Tue, May 15, 2018 at 6:32 PM, Sonibare, Kolawole <
kasonibare42_at_students.tntech.edu> wrote:

> Dear NAMD users,
>
>
> I am a new NAMD user and I intend to run a simulation of 120 molecules of
> an organic compound. Using some examples, I have been able to generate just
> a single molecule using psfgen. Please, how can I use this to get 120
> molecules? I have attached my tcl script.
>
>
> package require psfgen
> topology plant.top
> set name 2units
>
> resetpsf
> segment li {
> residue 1 SYR
> residue 2 GUAI
> }
>
> patch 4O5 li:1 li:2
>
> regenerate angles dihedrals
> coordpdb plant.pdb
> guesscoord
> writepdb $name.pdb
> writepsf $name.psf
>
>
> exit
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:19:55 CST