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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> Subject: Re: [gmx-users] vacuum right but melt collapse To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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 [email protected] 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 [EMAIL PROTECTED] 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
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