[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

[Antara mazumdar]

​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          = 250000        ; Number of steps to run (0.002 * 250000 =
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

-- 

Regards,

Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics & Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
--