[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled
Steven Neumann
s.neumann08 at gmail.com
Tue May 13 07:20:10 CEST 2014
Thanks a lot! So which combination of thermostat/barostat would provide a
proper ensemble without crashes? I am looking in the literature but did not
find anything.
On Tue, May 13, 2014 at 6:34 AM, Mark Abraham <mark.j.abraham at 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.neumann08 at 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.neumann08 at 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 <jalemkul at 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
> > >>
> > >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >> http://mackerell.umaryland.edu/~jalemkul
> > >>
> > >> ==================================================
> > >> --
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