@ 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 > > > > ------------------------------ > > Message: 5 > Date: Thu, 25 Apr 2013 13:34:21 +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=us-ascii > > > Did you visualise the system? T in function of time? Epot in function of time? > > As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = > 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 > if nstlist =10. > > On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <[email protected]> > wrote: > >> Hello all, >> >> I am trying to test the martini force field with PME for a charged system >> that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. >> My system works well, if i use the standard shift parameters (correct temp, >> and pressure). But for for the simulation with PME , the temp of the system >> decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K >> >> >> integrator = md >> dt = 0.020 >> nsteps = 10000 ; 200ps >> nstcomm = 10 >> comm-grps = >> ;refcoord_scaling = com >> >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 100 >> ;nstxtcout = 1000 >> xtc_precision = 100 >> ;xtc-grps = >> energygrps = AOT W ION OCT >> >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist = 1. >> >> ; PME parameters >> coulombtype = PME >> rcoulomb = 1.2 >> rvdw = 1.2 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> >> tcoupl = v-rescale >> tc-grps = AOT_W_ION OCT >> tau_t = 1.0 1.0 >> ref_t = 298 298 >> Pcoupl = berendsen >> Pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> >> ;gen_vel = no >> ;gen_temp = 0 >> ;gen_seed = 473529 >> >> >> ; MARTINI and CONSTRAINTS >> ; for ring systems and stiff bonds constraints are defined >> ; which are best handled using Lincs. >> >> constraints = none >> constraint_algorithm = Lincs >> unconstrained_start = no >> lincs_order = 4 >> lincs_warnangle = 3 >> >> >> Results obtained with W/ PME >> >> Statistics over 10001 steps using 1001 frames >> >> Energies (kJ/mol) >> Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip. >> 1.63789e+04 1.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 >> Potential Kinetic En. Total Energy Temperature Pressure (bar) >> -4.41367e+05 7.81801e+04 -3.63187e+05 2.90373e+02 -1.76470e+01 >> T-AOT_W_ION T-OCT >> 2.90629e+02 2.90357e+02 >> >> Results W:o PME >> >> Energies (kJ/mol) >> Bond G96Angle LJ (SR) Coulomb (SR) Potential >> 1.60482e+04 1.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 >> Kinetic En. Total Energy Temperature Pressure (bar) >> 8.02685e+04 -2.37777e+05 2.98129e+02 -3.07123e+01 >> >> Box-X Box-Y Box-Z >> 1.52926e+01 1.52926e+01 1.52926e+01 >> >> >> T-AOT_W_ION T-OCT >> 2.98141e+02 2.98129e+02 >> >> >> Did I miss something ? >> >> >> Note that for the moment i do not use the polarizable water model. >> >> Thanks for your help >> >> 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
