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?
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. >> 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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