VMD-L Mailing List

From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Tue May 17 2011 - 21:42:42 CDT

Dear axel,

Thank you very much for help!

Jianing
On Tue, 2011-05-17 at 10:44 -0400, Axel Kohlmeyer wrote:
> 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
> >
> >
>
>
>