[gmx-users] vacuum right but melt collapse

[Tsjerk Wassenaar]

Hi Ji Qing,

Write out the energies at every step and check which of the energy
contributions goes astray. This may give you a good clue to where
you're mistake is. Also, run through the topology again, by hand,
checking all bonds, angles, dihedrals, exclusion (implicit ones!),
etc.

Good luck,

Tsjerk

On 3/7/07, kitty ji <jiqing at iccas.ac.cn> wrote:
>
>
> Thanks Mark.
> But when one polymer chain was used, non-bonded interaction has already been
> there. Because one chain means C44H156O22.
> After all, I'd like to try more chains.
>
> Message: 1
> Date: Tue, 06 Mar 2007 17:01:52 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] vacuum right but melt collapse
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <45ED03D0.6010803 at anu.edu.au>
> Content-Type: text/plain; charset=GB2312
>
> kitty ji wrote:
> > Hi GMX user:
> >
> > A model for Poly(vinyl methyl ether) was built with OPLS force field (
> > all H ).
> >
> >
> >
> > When the model was run alone (a single chain) in vacuum, anything goes ok.
> >
> >
> >
> > But with 45 chains box, the system will be collapse with a little bond
> > elongates abnormal whatever in NVT or NPT.
> >
> >
> >
> > The relax time of pressure and temperature were adjust but no helpful.
> >
> >
> >
> > How can I found some possible reason and then fix it ? Any advise will
> > be appreciated.
>
> If an isolated molecule doesn't do anything strange, and two more more
> do, then you have a problem with inter-molecular interactions, i.e. the
> non-bonded ones. Try with just 2 chains to verify this... and look
> carefully at the atom types and the non-bonded parameters for them.
>
> Mark
>
>
>
> *************************************************
> Ji Qing
> Institute of Chemistry, Chinese Academy of Sciences
> Tel: 0086-10-62562894  ，82618423
> *************************************************
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623