OK, but with Berendsen you're also not observing physics. Your call. Mark
On Wed, May 14, 2014 at 3:50 AM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no > crashes observed. > > > On Tue, May 13, 2014 at 2:08 PM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > On May 13, 2014 7:21 AM, "Steven Neumann" <s.neuman...@gmail.com> wrote: > > > > > > Thanks a lot! So which combination of thermostat/barostat would > provide a > > > proper ensemble without crashes? > > > > Various - but only P-R for the barostat in GROMACS, so you must be > > conservative with REMD exchange period. That will depend on the system > and > > tau-p in a way that I expect nobody has studied. Hence avoiding NPT. > > > > > I am looking in the literature but did not > > > find anything. > > > > Some discussion in the manual. > > > > Mark > > > > > > On Tue, May 13, 2014 at 6:34 AM, Mark Abraham < > mark.j.abra...@gmail.com > > >wrote: > > > > > > > I would generally encourage the use of NVT REMD. However, note that > P-R > > > > does exhibit unstable oscillatory behaviour when not close to > > equilibrium. > > > > REMD is supposed to stay in equilibrium by design, but this gets > double > > > > crossed if the exchange period is too short with respect to the > > > > autocorrelation of whatever is relevant, because a subsequent > exchange > > is > > > > not from the right ensemble, so all bets are off. > > > > > > > > Mark > > > > On May 13, 2014 4:01 AM, "Steven Neumann" <s.neuman...@gmail.com> > > wrote: > > > > > > > > > Or just to switch to NVT? I guess it would be less realistic if one > > wants > > > > > to study extract the most likely conformation... > > > > > > > > > > > > > > > On Tue, May 13, 2014 at 3:26 AM, Steven Neumann < > > s.neuman...@gmail.com > > > > > >wrote: > > > > > > > > > > > What would you recommend then? Equilibrate with Berendsen > barostat > > and > > > > > > v-rescale thermostat? > > > > > > > > > > > > > > > > > > On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul <jalem...@vt.edu> > > > > wrote: > > > > > > > > > > > >> > > > > > >> > > > > > >> On 5/12/14, 3:58 AM, Steven Neumann wrote: > > > > > >> > > > > > >>> Dear Gmx Users, > > > > > >>> > > > > > >>> I am running REMD of a small protein in water. I have 36 > > > > temperatures. > > > > > >>> After minimization I equilibrate each with nvt and npt > ensemble. > > > > Then I > > > > > >>> start REMD with -multidir. The mdp: > > > > > >>> > > > > > >>> > > > > > >>> ; Run parameters > > > > > >>> integrator = md ; leap-frog integrator > > > > > >>> nsteps = 50000000 > > > > > >>> dt = 0.002 ; 2 fs > > > > > >>> ; Output control > > > > > >>> nstxout = 0 ; save coordinates every 0.2 ps > > > > > >>> nstvout = 0 ; save velocities every 0.2 ps > > > > > >>> nstenergy = 5000 ; save energies every 0.2 ps > > > > > >>> nstxtcout = 5000 > > > > > >>> nstlog = 5000 > > > > > >>> ; Bond parameters > > > > > >>> continuation = no ; first dynamics run > > > > > >>> constraint_algorithm = lincs ; holoyesmic constraints > > > > > >>> constraints = all-bonds ; all bonds (even heavy atom-H > > bonds) > > > > > >>> constrained > > > > > >>> lincs_iter = 1 ; accuracy of LINCS > > > > > >>> lincs_order = 4 ; also related to accuracy > > > > > >>> ; Neighborsearching > > > > > >>> ns_type = grid ; search neighboring grid cells > > > > > >>> nstlist = 5 ; 10 fs > > > > > >>> vdwtype = Switch > > > > > >>> rvdw-switch = 1.0 > > > > > >>> rlist = 1.4 ; short-range neighborlist cutoff (in > nm) > > > > > >>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in > > nm) > > > > > >>> rvdw = 1.2 ; short-range van der Waals cutoff (in > > nm) > > > > > >>> ewald_rtol = 1e-5 ; relative strenght of the > Ewald-shifted > > > > > >>> potential > > > > > >>> rcoulomb > > > > > >>> ; Electrostatics > > > > > >>> coulombtype = PME ; Particle Mesh Ewald for > long-range > > > > > >>> electrostatics > > > > > >>> pme_order = 4 ; cubic interpolation > > > > > >>> fourierspacing = 0.12 ; grid spacing for FFT > > > > > >>> ; Temperature coupling is on > > > > > >>> tcoupl = V-rescale ; modified > Berendsen > > > > > >>> thermostat > > > > > >>> tc_grps = Protein Water_and_ions ; two coupling groups - > > more > > > > > >>> accurate > > > > > >>> tau_t = 0.1 0.1 ; time constant, in > > ps > > > > > >>> ref_t = 320.12 320.12 ; reference > > > > > >>> temperature, > > > > > >>> one for each group, in K > > > > > >>> ; Pressure coupling is on > > > > > >>> pcoupl = Parrinello-Rahman ; pressure coupling > > is on > > > > > for > > > > > >>> NPT > > > > > >>> pcoupltype = isotropic ; uniform scaling > of > > box > > > > > >>> vectors > > > > > >>> tau_p = 2.0 ; time constant, in > > ps > > > > > >>> ref_p = 1.0 ; reference > pressure, > > in > > > > > bar > > > > > >>> compressibility = 4.5e-5 ; isothermal > > > > > compressibility > > > > > >>> of > > > > > >>> water, bar^-1 > > > > > >>> refcoord_scaling = com > > > > > >>> ; Periodic boundary conditions > > > > > >>> pbc = xyz ; 3-D PBC > > > > > >>> gen_temp = 320.12 > > > > > >>> DispCorr = EnerPres ; account for cut-off vdW scheme > > > > > >>> gen_seed = 173529 > > > > > >>> gen_vel = yes ; assign velocities from Maxwell > > distribution > > > > > >>> > > > > > >>> > > > > > >>> I get the error: step 12005: Water molecule starting at atom > 7030 > > can > > > > > not > > > > > >>> be settled. I tried to repeat it and I get the same error with > > > > another > > > > > >>> water molecule at different step. I am using Gmx 4.5.5 > > > > > >>> > > > > > >>> I tried minimization many times lowering the maximum force by > > > > steepest > > > > > >>> descent, make the time step 1fs in equilibtration but it does > not > > > > > help. I > > > > > >>> changed to force field as well and the same is happening. > Please, > > > > > advise. > > > > > >>> > > > > > >>> > > > > > >> NPT REMD is often unstable because when switching the > > configurations > > > > > >> between conditions, the barostats can become unstable. > > > > > >> > > > > > >> -Justin > > > > > >> > > > > > >> -- > > > > > >> ================================================== > > > > > >> > > > > > >> Justin A. Lemkul, Ph.D. > > > > > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > > >> > > > > > >> Department of Pharmaceutical Sciences > > > > > >> School of Pharmacy > > > > > >> Health Sciences Facility II, Room 601 > > > > > >> University of Maryland, Baltimore > > > > > >> 20 Penn St. > > > > > >> Baltimore, MD 21201 > > > > > >> > > > > > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > > >> http://mackerell.umaryland.edu/~jalemkul > > > > > >> > > > > > >> ================================================== > > > > > >> -- > > > > > >> Gromacs Users mailing list > > > > > >> > > > > > >> * Please search the archive at http://www.gromacs.org/ > > > > > >> Support/Mailing_Lists/GMX-Users_List before posting! > > > > > >> > > > > > >> * Can't post? 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