On 2/9/15 7:34 AM, Antara mazumdar wrote:
eRROR OBTAINED DURING NVT:
Water molecule starting at atom 673675 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
NVT CONDITIONS WERE :
n for B2AR-POPC system
define = -DPOSRES ; Protein is position restrained (uses the
posres.itp file information)
; Parameters describing the details of the NVT simulation protocol
integrator = md; Algorithm (md = molecular dynamics
[leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic
dynamics)
dt = 0.002 ; Time-step (ps)
nsteps = 25; Number of steps to run (0.002 * 25 =
500 ps)
; Parameters controlling output writing
nstxout = 1000 ; Write coordinates to output .trr file
every 2 ps
nstvout = 1000 ; Write velocities to output .trr file
every 2 ps
nstenergy = 1000 ; Write energies to output .edr file every
2 ps
nstlog = 1000 ; Write output to .log file every 2 ps
; Parameters describing neighbors searching and details about interaction
calculations
ns_type = grid ; Neighbor list search method (simple, grid)
nstlist = 5 ; Neighbor list update frequency (after
every given number of steps)
rlist = 1.2 ; Neighbor list search cut-off distance (nm)
rcoulomb= 1.2 ; Short-range Coulombic interactions
cut-off distance (nm)
rvdw= 1.2 ; Short-range van der Waals cutoff distance
(nm)
pbc = xyz ; Direction in which to use Perodic
Boundary Conditions (xyz, xy, no)
; Parameters for treating bonded interactions
continuation= no; Whether a fresh start or a continuation
from a previous run (yes/no)
constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
constraints = all-bonds ; Which bonds/angles to constrain
(all-bonds / hbonds / none / all-angles / h-angles)
lincs_iter = 2 ; Number of iterations to correct for
rotational lengthening in LINCS (related to accuracy)
lincs_order = 8 ; Highest order in the expansion of the
constraint coupling matrix (related to accuracy)
; Parameters for treating electrostatic interactions
coulombtype = PME ; Long range electrostatic interactions
treatment (cut-off, Ewald, PME)
pme_order = 4 ; Interpolation order for PME (cubic
interpolation is represented by 4)
fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using
PME (nm)
; Temperature coupling parameters
tcoupl = V-rescale ; Modified Berendsen thermostat
using velocity rescaling
tc-grps = Protein DOPC SOL_NA ; Define groups to be coupled
separately to temperature bath
tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant
(ps)
ref_t = 300 300 300 ; Group-wise reference temperature
(K)
; Pressure coupling parameters
pcoupl = no; Under NVT conditions pressure coupling is
not done
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Google will turn up about 27 million posts with the same problem. Please
investigate the list archive (that's why it's there).
-Justin
--
==
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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