nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your are happy that's ok :))
On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950 <[email protected]> wrote: > 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 -- 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
