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 = 5 ; 2 * 5 = 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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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