Hi Xavier, I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system.
Stephane ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole <[email protected]> Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 <[email protected]> wrote: > Xavier > > I have followed your suggestion and did a longer NPT equilibration with > smaller dt and ntlist values and It works. The Energy and Temp reach to > stables values as i want. > > thank you again for your help > > Stephane > > ------------------------------ > > Message: 2 > Date: Thu, 25 Apr 2013 14:17:00 +0000 > From: ABEL Stephane 175950 <[email protected]> > Subject: [gmx-users] Re: Martini with PME, temp two low > To: "[email protected]" <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > @ Vitaly > of course. I know that. My system is neutral but with charged particles (AOT > and Na+). > > @Xavier > I will try your suggestion and equilibrate my system for a longer period > > Thanks again > > Stephane > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Apr 2013 15:52:09 +0200 > From: XAvier Periole <[email protected]> > Subject: Re: [gmx-users] Martini with PME, temp two low > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=windows-1252 > > > Well ? 400 ps is rather small and you can expect deviations from so short > simulations if you start from an non-equilibrated system. I am not sure what > the void is but this indicates that your system might not be equilibrated ? > > You can try to decrease the time step and nstlist to see if you the drop of > temperature is due a flow of energy. > > On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 <[email protected]> > wrote: > >> Hello Xavier, >> >> Thank you for your response. >> >>>> nstlist = 10 and the rlist = 1.0 >> My mistake, i did not changes these values when i switched to PME, >> >> I have rerun the simulations for 400 ps in NPT with these changes and >> plotted Epot and Temp vs Time The Epot and Temp values are not stables. The >> average Temp of the system is better than previously but fluctuate around >> (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. >> >> I have also visualized my system at the end of the NPT run, the na+, >> water, surfactant, octane molecules form a slab with void >> >> What's wrong ? >> >> Stephane >> >> -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
