Sorry about forgetting the simulation time. They run for about 12 ns, at which point I stop them. They appear stable - the box vectors don't change a lot (which is surprising since the pressure sure does). Below is a complete mdp file.
title = Run1 cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 20000000 ; total 4ns. nstcomm = 1 nstxout = 50000 nstvout = 50000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Shift rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.6 ;pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = BMI PF6 tau_t = 0.1 0.1 ref_t = 300 300 nsttcouple = 1 ; Energy monitoring energygrps = BMI PF6 ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps = BMI PFF tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 100000 On Thu, Jan 20, 2011 at 3:49 PM, Justin A. Lemkul <[email protected]> wrote: > > > Denny Frost wrote: > >> from -1000 to 1000, depending on the system. The simulation box is 8x8x8 >> nm (roughly) and contains about 12,000 atoms >> >> > Are the systems even stable? Is there a trend in the pressure, or is it > stable at those values? It seems that the systems are either exploding or > imploding. How long are the simulations? Can you post a complete .mdp file? > > -Justin > > On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Denny Frost wrote: >> >> I am running a variety of NPT simulations with polar, non-polar, >> and ionic compounds. Although my results for density agree well >> with experimental values, the pressures I get from g_energy are >> off by 1 to 3 orders of magnitude. In the log file, the >> pressure fluctuates around a lot from -400 to 400 bar, which >> seems to be normal according to other posts on this list, but >> the average (which is what g_energy gives me) is not 1.0 bar, as >> I specified. Does anyone know how to correct this problem? >> >> >> What is the average value you're getting? How long are your >> simulations? >> >> -Justin >> >> >> Pressure coupling parameters: >> Pcoupl = berendsen >> pcoupltype = isotropic >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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