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.
Regards Vinoth On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <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 > 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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