On 28/12/11, Theodora García <theodoraaagar...@gmail.com> wrote:
> Hi > I just saw the article "Temperature Dependence of TIP3P, SPC, and TIP4P Water > from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density" > published in Journal of Computational Chemistry, Vol. 19, No. 10, 1179]1186 > (1998). It gives 0.985 for SPC at 25 C with different setup... perhaps 0.978 > is not so bad? Indeed. You should find the paper in which the parameterization of SPC was reported, and seek to reproduce the density reported there with a similar model physics. In general, a water model was probably parameterized to reproduce a set of observables reasonably well, and it does none of them perfectly. In practice, around 0.98 is normal enough in my recollection. Mark > > > > > > > > > On Wed, Dec 28, 2011 at 9:34 AM, Theodora García <theodoraaagar...@gmail.com> > wrote: > > > > 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(tel:%2B46184714205). > > > sp...@xray.bmc.uu.se > > > http://folding.bmc.uu.se(http://folding.bmc.uu.se/) > > > -- > > > 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 > > > > > > > > > > > > > > > > >
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