Hi Mark How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more clearly? It will be of more useful to me to understand the concept.
One more thing, density (from g_energy command) of water is found to low (expected 1000) after NPT is equilibration. why? given below is my average density value. Can i proceed with this density value? Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Density (SI) 979.37 14.3238 14.2431 -0.0525784 -5.25789 Regards Vinoth On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote: > > I am using the semiisotropic pressure scaling because i want the box size > to remain the same as that of the original box size in X and Y axis and want > to change it only on the Z axis. I am doing this because at a latter stage i > want to create an interface with organic solvent where i need the cross > sections (X and Y axis length) of both the box should be the same. > > what i should do now get the pressure of 1 bar? > > > 7 +/- 500 *is* approximately 1 bar, and hardly any better an approximation > than 1 +/- 500. If you want lower fluctuations, use a larger system and run > for a much longer time. Or, since you'll have to re-equilibrate once you > combine the solvent boxes, don't bother. > > Mark > > > Has no one has got the pressure of water to be close to 1 bar in GROMACS > till now? > > Regards > Vinoth > > On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel < > sp...@xray.bmc.uu.se> wrote: > >> On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote: >> >>> >>> Hi Mark >>> >>> I read the link before posting the question. even though the fluctation >>> is between 500-600 (as said in the link) bar the average pressure is >>> around 7.4 bar. my concern is the average pressure?. Because at a latter >>> stage i am going to combine this water box with another organic solvent >>> and i want to avoid any complications there. >>> >> >> Think again of what you just wrote. Your value is 7 +/- 500. In fact >> according to normal statistical rules you should round the value of 7 to 0. >> If you want more accurate number you could increase the box size by a factor >> of 100. >> >> By the way, why are you using semiisotropic pressure scaling in a water >> box? >> >> >>> Regards >>> Vinoth >>> >>> On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au>> wrote: >>> >>> On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote: >>> >>> Hi Gromacians >>> >>> I want to do equilibration of water (spc model) first in the NVT >>> ensemble and then in the NPT ensemble to maintain a temperature >>> of 300K and a pressure of 1 bar respectively. The NVT >>> equilibration works fine and the average temperature turns out >>> to be 299.229 K. >>> >>> Energy Average RMSD Fluct. >>> Drift Tot-Drift >>> ------------------------------ >>> ------------------------------------------------- >>> Temperature 299.229 10.3092 10.2463 >>> 0.0393873 3.93877 >>> Heat Capacity Cv: 12.494 J/mol K (factor = 0.00118698) >>> >>> when i do NPT equilibration i am not getting the desired >>> pressure as 1 bar or atleast close to 1 bar (between 1-1.4 bar). >>> In the mdp file i used semiisotropic pressure coupling type >>> because i want to fix the length of the box same on two axis as >>> that of the original box size and want to change it only on one >>> axis. can any one tell me why iam not getting the desired >>> pressure of 1 bar?. >>> >>> >>> This looks normal for a smallish water system over 100ps. See >>> http://www.gromacs.org/Documentation/Terminology/Pressure >>> >>> Mark >>> >>> >>> >>> Energy Average RMSD Fluct. >>> Drift Tot-Drift >>> >>> >>> ------------------------------------------------------------------------------- >>> Pressure (bar) 7.4339 574.052 573.574 >>> 0.812129 81.2138 >>> >>> Given below is my mdp file (NPT equilibration). any help is >>> highly appreciated. >>> >>> title = DCE NVT equilibration >>> cpp = usr/bin/cpp >>> integrator = md >>> nsteps = 100000 >>> dt = 0.001 >>> nstxout = 100 >>> nstvout = 100 >>> nstenergy = 100 >>> nstlog = 100 >>> ns_type = grid >>> nstlist = 1 >>> rlist = 1.0 >>> coulombtype = PME >>> rcoulomb = 1.0 >>> vdwtype = Cut-off >>> rvdw = 1.0 >>> pme_order = 4 >>> fourierspacing = 0.16 >>> pbc = xyz >>> tcoupl = V-rescale >>> tc-grps = system >>> tau_t = 0.1 >>> ref_t = 300 >>> pcoupl = berendsen >>> pcoupltype = semiisotropic >>> tau_p = 0.5 >>> ref_p = 1.0 1.0 >>> compressibility = 0.0 4.5e-5 >>> DispCorr = Enerpres >>> gen_vel = yes >>> gen_temp = 300 >>> gen_seed = 173529 >>> >>> Regards >>> Vinoth >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto: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 >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> >> -- >> 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 >> 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 >> > > > > -- > 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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