Thank your for your answer ! Actually yes, annealing is just a preparatory step, so I'll just keep Berendsen barostat for the equilibration. I was just wondering about the behaviour of Parrinello-Rahman. Thanks !
Baptiste 2013/5/21 Justin Lemkul <jalem...@vt.edu> > > > On 5/21/13 7:55 AM, Baptiste Demoulin wrote: > >> Dear Gromacs users, >> >> I am trying to simulate a large systems embeded in a membrane (roughly >> 360,000 atoms). I would like to equilibrate it at 300K and 1 atm. To this >> mean, I use simulated annealing to slowly warm up the system from 50 to >> 300K, under NPT conditions. >> >> For the simulation, I use position restraints on the heavy atoms on the >> protein, and stronger constraints on the metallic core, and LINCS to >> constrain all the bonds, and 2 fs timestep. >> >> My problem is that when I use Parrinello-Rahman barostat for the >> simulation, I got LINCS warning concerning the restrained metallic core. >> However, using Berendsen barostat for the same system, same input, seems >> to >> work fine, (at least for the 200,900 steps I did until now). I thus tried >> various modifications, such as changing the coupling tau_p, running first >> a >> pure NVT at 50K for 2 ps, and then warming, but that did not work... Is >> there an incompatibility between Parrinello-Rahman and simulated annealing >> ? >> >> > Parrinello-Rahman allows for much wider fluctuations than the Berendsen > algorithm, so I can see how warming the system may cause problems unless it > is very well equilibrated beforehand. Assuming that the annealing step is > a preparatory step, there is no compelling need to use P-R, is there? If > there is, you may just have to do the annealing over a much longer time > period such that the change in temperature is (very) long with respect to > tau_p, to allow for the barostat to adjust to changing conditions. > > -Justin > > > Here is my input: >> >> define = -DPOSRES -DPOSRES_CORE >> integrator = md >> continuation = no ; first dynamics run >> nsteps = 1500000 >> dt = 0.002 >> >> nstcomm = 1 >> comm-mode = linear >> comm-grps = Protein_POPC SOL_NA_CL >> >> pbc = xyz >> nstlist = 10 >> ns-type = grid >> rlist = 1.0 >> rlistlong = 1.6 ; the force on a particle which falls within >> rlist and rlistlong is calculated during the pair list update and retained >> during nslist steps >> coulombtype = pme >> rcoulomb = 1.0 >> vdwtype = cut-off >> rvdw = 1.4 >> DispCorr = EnerPres >> >> nstxtcout = 10 >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 10 >> >> constraints = all-bonds >> constraint-algorithm = lincs >> >> tcoupl = V-rescale >> tc-grps = Protein POPC SOL_NA_CL >> tau_t = 0.1 0.1 0.1 >> ref_t = 300 300 300 >> >> pcoupl = Parrinello-Rahman >> pcoupltype = semiisotropic >> compressibility = 4.5e-5 4.5e-5 >> tau_p = 10.0 >> ref_p = 1.0 1.0 >> >> refcoord_scaling = com >> >> gen_vel = no >> gen_temp = 50 >> gen_seed = -1 >> >> annealing = single single single >> annealing_npoints = 2 2 2 >> annealing_time = 0 2000 0 2000 0 2000 >> annealing_temp = 50 300 50 300 50 300 >> >> Thank you very much for your help ! >> >> Baptiste >> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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