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

[Justin Lemkul]

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

==================================================