[gmx-users] error while equilibration

[Justin Lemkul]

On 3/18/15 12:01 PM, ananyachatterjee wrote:
>
> I am trying to simulate RNA in water. I have minimized the system with steepest
> Decent for 2000 steps and then with Conjugate gradient for till the energy
> coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am
> getting following error
>

What's the actual output in terms of Epot and Fmax?  What force field are you using?

> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538
>
> Fatal error:
> 11 particles communicated to PME node 3 are more than 2/3 times the cut-off out
> of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> My nvt.mdp file contain
>
> title       = RNA complex NVT equilibration
> define      = -DPOSRES  ; position restrain
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 0.2 ps
> nstvout     = 100       ; save velocities every 0.2 ps
> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps  = RNA SOL NA
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic 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
> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)

I doubt these settings are right for any of the reliable nucleic acid force 
fields I know of, but you'll have to answer the question above.

> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = RNA SOL NA  ; two coupling groups - more accurate

Don't couple solvent and ions separately.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

-Justin

> tau_t       = 0.1   0.1 0.1                     ; time constant, in ps
> ref_t       = 310   310 310                    ; reference temperature, one for
> each group, in K
> ; Pressure coupling
> pcoupl      = no        ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 310       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Please tell me where I am doing wrong.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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