Thank you very much for your advice... I have tried including dispcorr = enerpres in my mdp file and the density increased a bit in a timescale of 5 ns but it is still far from the value expected for pure water. These are the new results:
Statistics over 2500001 steps [ 0.0000 thru 5000.0000 ps ], 3 data sets All averages are exact over 2500001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Temperature 298 2.67563 2.67534 2.70867e-05 0.135433 Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622 Density (SI) 978.114 4.10621 4.10412 -9.08266e-05 -0.454133 Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05) Isothermal Compressibility: 5.40447e-05 /bar Adiabatic bulk modulus: 18503.2 bar I guess I should get 1000 g/cm^3 Any other suggestion? On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel <sp...@xray.bmc.uu.se>wrote: > On 2011-12-27 17:57, Theodora García wrote: > >> Dear all >> I am starting some MD simulations aimed to calculate the volume of a >> solute in water as a function of the concentration. First I ran a >> simulation of a box with 4124 SPC water molecules (similar number of >> molecules that will be later used with my solute) for which I got the >> following results after ~7.5 ns: >> > > dispcorr = enerpres > > >> Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets >> All averages are exact over 3762001 steps >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> ------------------------------**------------------------------** >> ------------------- >> Temperature 298 125.156 125.156 1.9202e-05 >> 0.144476 >> Volume 126.908 53.2917 53.2917 5.61522e-06 >> 0.0422489 >> Density (SI) 972.142 408.201 408.201 -4.30887e-05 >> -0.324199 >> Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) >> Isothermal Compressibility: 0.543909 /bar >> Adiabatic bulk modulus: 1.83854 bar >> >> Why am I obtaining so low density? The density seems to be constant over >> that timescale. >> >> This is my mdp file: >> >> constraints = all-bonds >> integrator = md >> dt = 0.002 >> nsteps = 2500000 >> >> nstxout = 5000 >> nstvout = 50000 >> nstenergy = 1000 >> nstxtcout = 5000 >> energygrps = SOL >> nstlist = 5 >> >> ns_type = grid >> rlist = 1.2 >> rcoulomb = 1.2 >> rvdw = 1.2 >> coulombtype = PME >> fourierspacing = 0.15 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> >> Tcoupl = nose-hoover >> tau_t = 0.1 >> tc-grps = SOL >> ref_t = 298 >> >> Pcoupl = Parrinello-Rahman >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> pcoupltype = isotropic >> >> gen_vel = yes >> gen_temp = 298 >> gen_seed = -1 >> >> >> Thanks in advance for any help... >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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