Hi Kitty, OPLS was developed (IIRC) for use with a cut-off of 1.2 nm. Not shorter, not longer. If you set the cut-off higher, you introduce additional force components; noise, artefacts, not precision. It may be good to do some reading about force fields and the parameterization thereof.
The reaction field is a correction for the neglect of electrostatic interaction beyond the cut off. It should be used when using a GROMOS force field, as those are parameterized for use with it. Regarding OPLS, I'm not sure. I thought it was not parameterized for use with RF, but either a plain cut-off or a cut-off with a switch function. You should check the OPLS papers to be sure. By the way, please keep discussions on the list... In that way, it is publicly archived, which potentially saves us a lot of trouble answering the same questions over and over. Cheers, Tsjerk On 3/9/07, kitty ji <[EMAIL PROTECTED]> wrote:
Thanks for your reply. The force field I used here is OPLS. Increasing the cutoff means to increase the precision of caluculation not "underlying cause". Therefore it is acceptable. In addition, it is said that cutoff 9 angstrom is not enough for electricity calculation. what is using reaction-field? I thought it was not used here. ----- Original Message ----- From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> To: "kitty ji" <[EMAIL PROTECTED]>; "Discussion list for GROMACS users" <[email protected]> Sent: Thursday, March 08, 2007 10:34 PM Subject: Re: Re: [gmx-users] vacuum right but melt collapse 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 <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> > Subject: Re: Re: [gmx-users] vacuum right but melt collapse > To: "kitty ji" <[EMAIL PROTECTED]>, "Discussion list for GROMACS > users" <[email protected]> > Message-ID: > <[EMAIL PROTECTED]> > 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 <[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 > > _______________________________________________ > 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
-- 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 [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
