[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

Steven Neumann s.neumann08 at gmail.com
Fri May 16 07:37:44 CEST 2014


But with NVT REMD at high temperatures the pressure goes very high so the
conformational space sampled is not reliable.


On Wed, May 14, 2014 at 3:12 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> > > > > > >>
> > > > > > >> ==================================================
> > > > > > >> --
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