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

[Steven Neumann]

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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