VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Tue May 17 2011 - 21:32:52 CDT

Dear John,

Thank you very much for help.

Jianing

On Tue, 2011-05-17 at 10:09 -0500, John Stone wrote:
> 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
>