[gmx-users] vacuum right but melt collapse

[Tsjerk Wassenaar]

Hi Kitty,

Such a solution is unsatisfactory, as it seems that you're masking an
underlying cause. Now, I'm not sure of your other parameters, but when
using a cut-off (do you use reaction-field) you would usually (gromos
force field) use a twin-range of 0.9/1.4, which is what the force
field was parameterized for.

If you look at the energies in order to find the cause of a crash, you
want to look for the energy term first displaying strange behaviour.
You also may want to try setting the neighbour list update to every
step.

And please, don't use html formatted e-mails... :)

Hope it helps,

Tsjerk


On 3/8/07, kitty ji <jiqing at iccas.ac.cn> wrote:
>
>
>
>
> 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
> > *************************************************
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> --
> 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
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>


-- 
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