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

[Mark Abraham]

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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