[gmx-users] (no subject)

[Padmani Sandhu]

Hello,


I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
in POPC lipid membrane. After energy minimizing of complex, I am facing
problem with NVT equilibration step. mdrun crashed with following error:


"12 particles communicated to PME node 4 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."




These are the parameters used in nvt.mdp file:

title		= NVT equilibration

define		= -DPOSRES_LIPID -DPOSRES
-DPOSRES_WATER	; position restrain the protein

; 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

; 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 cels

nstlist		= 5		    ; 10 fs

rlist		= 1.2		; short-range neighborlist cutoff
(in nm)

rcoulomb	= 1.2		; short-range electrostatic
cutoff (in nm)

rvdw		= 1.2		; short-range van der Waals cutoff
(in nm)

; Electrostatics

coulombtype	= PME		; Particle Mesh Ewald for
long-range electrostatics

pme_order	= 4		    ; cubic interpolation

fourierspacing	= 0.16		; grid spacing for FFT

; Temperature coupling is on

tcoupl		= V-rescale	            ; modified
Berendsen thermostat

tc-grps		= Protein_LMT POPC Water_and_ions	;
three coupling groups - more accurate

tau_t		= 0.1	0.1	0.1	        ; time constant, in
ps

ref_t		= 271 	271	271	        ; reference
temperature, one for each group, in K

; Pressure coupling is off

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	= 271		; temperature for Maxwell
distribution

gen_seed	= -1		; generate a random seed

; COM motion removal

; These options remove motion of the
protein/bilayer relative to the solvent/ions

nstcomm		= 1

comm-mode	= Linear

comm-grps	= Protein_LMT_POPC Water_and_ions




Please help me...!!!!




-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*