And ? sorry but i do not understand... Stephane
------------------------------ Message: 2 Date: Thu, 25 Apr 2013 15:39:12 +0200 From: "Dr. Vitaly Chaban" <[email protected]> Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users <[email protected]> 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 <[email protected]> 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 <[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
