[gmx-users] rotation of atoms by more than 90 degrees & LINCS Warnings

[sagar bathla]

Dear all,

My system consists of 2 orthorhombic parallel graphene sheets in a big
triclinic box filled with water. when i am trying to run equillibration
then i am getting too many lincs warnings and simulation has been getting
crashed everytime. i have put retraint on all atoms of graphene but still
this problem is occuring again.

My .mdp file looks like this
title           = OPLS Graphene IN WATER NVT equilibration
define          = -DPOSRES -DFLEXIBLE   ; position restrain the protein

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 500000                ; 2 * 500000 = 1000 ps

dt                  = 0.002             ; 2 fs

; Output control
nstxout         = 1000          ; save coordinates every 1.0 ps
nstvout         = 1000          ; save velocities every 1.0 ps
nstenergy       = 1000          ; save energies every 1.0 ps
nstlog          = 1000          ; update log file every 1.0 ps

; Bond parameters
continuation            = yes           ; 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
lincs-warnangle             = 90

; Neighborsearching
vdw-modifier            = Force-switch
cutoff-scheme   = Verlet
ns_type             = grid              ; search neighboring grid cells
nstlist             = 10                ; 20 fs, largely irrelevant with
Verlet
rcoulomb            = 1.2               ; short-range electrostatic cutoff
(in nm)
rvdw                = 1.2
rlist               = 1.2               ; short-range van der Waals cutoff
(in nm)
rvdw-switch         = 1.0
; 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          = nose-hoover               ; nose-hoover thermostat
tc-grps         = GRA SOL       ; two coupling groups - more accurate
tau_t           = 0.1     0.1           ; time constant, in ps
ref_t           = 300     300           ; 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
periodic-molecules = yes

; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme

; number of steps for center of mass motion removal =
comm-mode                = Linear
nstcomm                  = 1
comm-grps                = GRA SOL
; Velocity generation
gen_vel         = no            ; assign velocities from Maxwell
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed

;non equillibrium md
freezegrps: GRA
freezedim: Y Y Y
 i have tried various things but nothing is working.
please help to solve this problem

Regards
Sagar Bathla