Dear Justin: Thanks for your response. Here is the complete my .mdp file:
title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 2500000 ; total 10ns. nstcomm = 1 nstxout = 50000 nstvout = 50000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps = PDM 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, May 14, 2009 at 4:06 PM, Justin A. Lemkul <[email protected]> wrote: > > > Yanmei Song wrote: > >> Dear All: >> >> I have question about the pressure coupling. I have done a 10ns simulation >> with 19800 atoms for 120 large molecules using the following pressure >> coupling. >> >> Tcoupl = berendsen >> tc_grps = PDM >> tau_t = 0.1 >> ref_t = 300 >> >> Pcoupl = berendsen >> pcoupltype = isotropic >> ;pc-grps = PDM >> tau_p = 1.0 >> ref_p = 1.0 >> compressibility = 4.5e-5 >> >> Then I did g_energy for the last 3ns and got the results: >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> >> ------------------------------------------------------------------------------- >> Potential -98061 0 0 0.61668 >> 1850.04 >> Temperature 303.561 109.602 109.602 0.000181791 >> 0.545372 >> Pressure (bar) 4.4884 11110.8 11109.8 -0.169835 >> -509.506 >> >> For such a long run the pressure drift is still too much and seem hasn't >> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did >> a similar system by using the same method. it just take 2 or 3ns to reach >> the equilibrium. and the pressure is around 1.01after the run. The only >> difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 >> is too large to make the system running slower. Or the pressure coupling >> method is not working well. Anyone can give me any suggestions? >> >> >> > I think it will depend on the interplay of other parameters as well. > Posting a complete .mdp file may be more helpful. > > -Justin > > -- >> Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
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