PME should NOT be used with charged systems, for obvious reasons.
On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950 <stephane.a...@cea.fr>wrote: > And ? sorry but i do not understand... > > Stephane > > ------------------------------ > > Message: 2 > Date: Thu, 25 Apr 2013 15:39:12 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > Subject: Re: [gmx-users] Martini with PME, temp two low > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAPXdD+bDiuQWG_3eWZ_0yb= > aynlaaf08vt46usel4wk_bjg...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hmmm.... > > Aren't the keywords here "charged system" + "PME"? > > > Dr. Vitaly Chaban > > > > On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > > > > 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 <stephane.a...@cea.fr> > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists