Dear Shanshan Qin, Please keep the discussions on the list. That way, you can benefit from the input from others as well and the discussion will be archived. Note I didn't forward your structures/topologies, since I don't know whether it's okay that that information is archived too...
Best, Tsjerk ---------- Forwarded message ---------- From: 秦姗姗 <[EMAIL PROTECTED]> Date: Aug 29, 2007 1:51 PM Subject: Re: Re: [gmx-users] how to deal with large pressure fluctuation To: Tsjerk Wassenaar <[EMAIL PROTECTED]> Dear Wassenaar: Thanks vey much for your kind reply. I constructed a lipid bilayer and solvated it in the water and energy minimized them. I ran NVT simulation using time step 0.0001 ps.After 50 ps, water just came into the bilayer! However I can't run NPT at the very beginning,because it would definitely crash.I put all my input files in the attachment, will you have a look at it?All the forcefield parameters were downloaded from Tieleman's website. Looking forward to your reply. Regards Shanshan Qin > -----Original Message----- > From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> > Date: Wed, 29 Aug 2007 10:58:56 +0200 > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Subject: Re: [gmx-users] how to deal with large pressure fluctuation > Hi Q733, > > The large pressure fluctuation is not the cause of your problem. In > fact, the pressure will show large fluctuations in MD anyway and this > has been discussed on the mailing list numerous times and can be found > on the Gromacs Wiki. That your simulation crashes is caused by > something else, which I can not assess from the information you have > provided. Unstable system? Not minimized enough? Overlapping atoms? > The Fmax suggests otherwise, but something's wrong. Check your > starting structure and your topology. > > To start with, you might want to paste your .mdp file. > > Cheers, > > Tsjerk > > On 8/29/07, Q733 <[EMAIL PROTECTED]> wrote: > > Dear gmx-users: > > > > I made a lipid bilayer fully hydrated by water,without water in the > > lipid hydrophobic tails.Then I minimized the energy to Fmax=132.5,then I > > ran NVT md for 200ps.However when > > I wanted to run NPT simulation, the pressure fluctuation was as high as > > 1.33*10E+05,it crashed very easily. > > Does anyone know how to deal with large pressure fluctuation?I tried to > > enlarge tp,however,it was of no use. > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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
grompp.mdp
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