<DIV> </DIV><DIV> </DIV><SPAN>On 28/12/11, <B class=name>Theodora García </B><theodoraaagarcia@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CACxyT-zCCVdgMyCbaatY78SLkftLyNt=XqHEcSZ+g2TzLO5wNA@mail.gmail.com type="cite">Hi<br />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?</BLOCKQUOTE>
<DIV> </DIV><DIV>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.</DIV><DIV> </DIV><DIV>Mark </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CACxyT-zCCVdgMyCbaatY78SLkftLyNt=XqHEcSZ+g2TzLO5wNA@mail.gmail.com type="cite">
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<DIV class=gmail_quote>On Wed, Dec 28, 2011 at 9:34 AM, Theodora García <SPAN dir=ltr><<a href="mailto:theodoraaagarcia@gmail.com" >theodoraaagarcia@gmail.com</A>></SPAN> wrote:<br />
<BLOCKQUOTE style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>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:<br /><br />Statistics over 2500001 steps [ 0.0000 thru 5000.0000 ps ], 3 data sets<br />All averages are exact over 2500001 steps
<DIV class=im><br /><br />Energy Average RMSD Fluct. Drift Tot-Drift<br />-------------------------------------------------------------------------------<br /></DIV>Temperature 298 2.67563 2.67534 2.70867e-05 0.135433<br />Volume 126.133 0.529594 0.529323 1.17324e-05 0.0586622<br />Density (SI) 978.114 4.10621 4.10412 -9.08266e-05 -0.454133<br />Heat Capacity Cv: 12.4733 J/mol K (factor = 8.06157e-05)<br />Isothermal Compressibility: 5.40447e-05 /bar<br />Adiabatic bulk modulus: 18503.2 bar<br /><br />I guess I should get 1000 g/cm^3<br /><br />Any other suggestion?
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<DIV class=gmail_quote>On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel <SPAN dir=ltr><<a href="mailto:spoel@xray.bmc.uu.se" target=1 >spoel@xray.bmc.uu.se</A>></SPAN> wrote:<br />
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<DIV>On 2011-12-27 17:57, Theodora García wrote:<br />
<BLOCKQUOTE style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>Dear all<br />I am starting some MD simulations aimed to calculate the volume of a<br />solute in water as a function of the concentration. First I ran a<br />simulation of a box with 4124 SPC water molecules (similar number of<br />molecules that will be later used with my solute) for which I got the<br />following results after ~7.5 ns:<br /></BLOCKQUOTE><br /></DIV>dispcorr = enerpres
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<BLOCKQUOTE style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote><br />Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets<br />All averages are exact over 3762001 steps<br /><br />Energy Average RMSD Fluct. Drift<br />Tot-Drift<br />------------------------------<U></U>------------------------------<U></U>-------------------<br />Temperature 298 125.156 125.156 1.9202e-05<br />0.144476<br />Volume 126.908 53.2917 53.2917 5.61522e-06<br />0.0422489<br />Density (SI) 972.142 408.201 408.201 -4.30887e-05<br />-0.324199<br />Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389)<br />Isothermal Compressibility: 0.543909 /bar<br />Adiabatic bulk modulus: 1.83854 bar<br /><br />Why am I obtaining so low density? The density seems to be constant over<br />that timescale.<br /><br />This is my mdp file:<br /><br />constraints = all-bonds<br />integrator = md<br />dt = 0.002<br />nsteps = 2500000<br /><br />nstxout = 5000<br />nstvout = 50000<br />nstenergy = 1000<br />nstxtcout = 5000<br />energygrps = SOL<br />nstlist = 5<br /><br />ns_type = grid<br />rlist = 1.2<br />rcoulomb = 1.2<br />rvdw = 1.2<br />coulombtype = PME<br />fourierspacing = 0.15<br />pme_order = 4<br />ewald_rtol = 1e-5<br />optimize_fft = yes<br /><br />Tcoupl = nose-hoover<br />tau_t = 0.1<br />tc-grps = SOL<br />ref_t = 298<br /><br />Pcoupl = Parrinello-Rahman<br />tau_p = 0.5<br />compressibility = 4.5e-5<br />ref_p = 1.0<br />pcoupltype = isotropic<br /><br />gen_vel = yes<br />gen_temp = 298<br />gen_seed = -1<br /><br /><br />Thanks in advance for any help...<br /><br /><br /></BLOCKQUOTE><br /><br /></DIV></DIV><SPAN><FONT color=#888888>-- <br />David van der Spoel, Ph.D., Professor of Biology<br />Dept. of Cell & Molec. Biol., Uppsala University.<br />Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" target=1 value="+46184714205" >+46184714205</A>.<br /><a href="mailto:spoel@xray.bmc.uu.se" target=1 >spoel@xray.bmc.uu.se</A> <a href="http://folding.bmc.uu.se/" target=1 >http://folding.bmc.uu.se</A><br />-- <br />gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target=1 >gmx-users@gromacs.org</A><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=1 >http://lists.gromacs.org/<U></U>mailman/listinfo/gmx-users</A><br />Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=1 >http://www.gromacs.org/<U></U>Support/Mailing_Lists/Search</A> before posting!<br />Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target=1 >gmx-users-request@gromacs.org</A>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target=1 >http://www.gromacs.org/<U></U>Support/Mailing_Lists</A><br /></FONT></SPAN></BLOCKQUOTE></DIV><br /></DIV></DIV></BLOCKQUOTE></DIV><br /></DIV></BLOCKQUOTE>
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