[gmx-users] LINCS error while running NVT equlibration

[Deep Bhattacharya]

Hello,

I am trying to run a NVT equilibration of 2.5 ns of my protein-carbohydrate
complex but its failing because I am getting this error message all the
time

Step 33, time 0.033 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002814, max 0.053588 (between atoms 1553 and 1552)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1553   1552   90.0    0.1000   0.1054      0.1000

Step 34, time 0.034 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000318, max 0.005474 (between atoms 1553 and 1552)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1553   1552   70.0    0.1054   0.1005      0.1000

Step 35, time 0.035 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000320, max 0.005247 (between atoms 1553 and 1552)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1553   1552   79.9    0.1005   0.0995      0.1000

nvt.mdp
title       = 123
define      = -DPOSRES -DPOSRES_LIGAND ; Run parameters
integrator  = md-vv        ; leap-frog integrator
nsteps      = 2500000     ; 0.001 * 2500000 = 2500 ps
dt          = 0.001     ; 1 fs
; Output control
nstxout             = 5000         ; suppress .trr output
nstvout             = 5000         ; suppress .trr output
nstenergy           = 5000    ; save energies every 1000.0 ps
nstlog              = 5000      ; update log file every 1000.0 ps
nstxtcout = 5000
xtc_precision = 100
energygrps  = Protein LIG SOL
; 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        ;
rcoulomb        = 0.9
rvdw            = 1.4
coulombtype     = PME       ; Particle Mesh Ewald for long-
rlistlong      = 1.4
rlist          = 0.9
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
periodic_molecules = yes
; Temperature coupling
tcoupl      = nose-hoover                     ; modified Berendsen
thermostat
tc-grps     = Protein_LIG Water_and_ions    ; two coupling groups - more
accurate
tau_t       = 2.0   2.0                     ; time constant, in ps
ref_t       = 300   300                     ; 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
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed


Please help.
-- 
Deep Bhattacharya.