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? 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 >
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