VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 17 2011 - 10:09:55 CDT

Hi,
  VMD _will_ write angles/dihedrals/impropers and cross-terms,
but only if they were loaded from another file. It will warn you
if you write a PSF that lacks these components. There are programs
out there (e.g. Willy Wriggers SITUS package) that read PSF files
for other purposes that do not need all of the fields that would be
required for an MD simulation, and this is why VMD allows you to write
incomplete PSF files, though it warns you about it.
Obviously you cannot use an incomplete PSF file for a full MD simulation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 17, 2011 at 09:54:54PM +0800, jnsong 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?
>
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078