VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 17 2011 - 09:44:26 CDT

On Tue, May 17, 2011 at 9:54 AM, jnsong <jnsong_at_itcs.ecnu.edu.cn> wrote:
> Dear all,
>
> As we all know, the PSF files produced by "$sel writepsf" function in
> VMD will lack angles, dihedrals, impropers, and cross-terms. If I use
> this kind psf to perform MD simulation using NAMD, will the results of
> MD simulation be different from the psf generated by psfgen?

what do you expect?
will a force field be the same if you leave out
a significant chunk of its components?

this is a trivial question and you should answer it by yourself.
if you cannot answer it yourself, you should not run an MD.

axel.

>
> Thank you very much!
>
> Jianing
>
> --
> Jianing Song
> Ph. D. Student
> Institute of Theoretical and Computational Sciences
> Dept. Phys.
> East China Normal University
> 200062
> 3663 North Zhongshan Road
> Shanghai, P. R. China
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.