[gmx-users] vacuum right but melt collapse

[kitty ji]

Tsjerk Wassenaar, thank you very much for you suggestion even if most of them have been manipulated. 

 

"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."

when the explosion happened, the energy of bond, angle and potential will were increase. And the topology has been checked several times. 

 

 

Now I increase the cutoff of VDW & Coulomb from 0.9 to 1.5. The system looks ok from last night to this time. If the problem is fixed, I conclude that cutoff 0.9 is not enough for electric system.



Hope this conclusion is helpful for GMX users.




Message: 2
Date: Wed, 7 Mar 2007 17:49:30 +0100
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: Re: [gmx-users] vacuum right but melt collapse
To: "kitty ji" <jiqing at iccas.ac.cn>, "Discussion list for GROMACS
users" <gmx-users at gromacs.org>
Message-ID:
<8ff898150703070849r59cb8a8dr60b894a881fcc331 at mail.gmail.com>
Content-Type: text/plain; charset=GB2312; format=flowed

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
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