[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled
Mark Abraham
mark.j.abraham at gmail.com
Wed May 14 09:12:46 CEST 2014
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.neumann08 at 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.abraham at gmail.com
> >wrote:
>
> > On May 13, 2014 7:21 AM, "Steven Neumann" <s.neumann08 at 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.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
> > > > > >>
> > > > > >> ==================================================
> > > > > >> --
> > > > > >> Gromacs Users mailing list
> > > > > >>
> > > > > >> * Please search the archive at http://www.gromacs.org/
> > > > > >> Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >>
> > > > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >>
> > > > > >> * For (un)subscribe requests visit
> > > > > >>
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > > >> send a mail to gmx-users-request at gromacs.org.
> > > > > >>
> > > > > >
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list