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Hi, I am simulating MraY protein which is a protein found in thermophiles. At the step of NVT i am getting error for “Too many LINCS warnings (5691)

If you know what you are doing you can adjust the lincs warning threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,

but normally it is better to fix the problem”

Before this, I didn’t get this type of error. How should I solve this error ? I am using POPE lipid and TIP3 water. My system looks fine (noting unusal).

NVT parameters

Input Parameters:

integrator = md

tinit = 0

dt = 0.02

nsteps = 500000

init-step = 0

simulation-part = 1

comm-mode = Linear

nstcomm = 100

bd-fric = 0

ld-seed = 1386368483

emtol = 10

emstep = 0.01

niter = 20

fcstep = 0

nstcgsteep = 1000

nbfgscorr = 10

rtpi = 0.05

nstxout = 500

nstvout = 500

nstfout = 0

nstlog = 500

nstcalcenergy = 100

nstenergy = 500

nstxout-compressed = 0

compressed-x-precision = 1000

cutoff-scheme = Verlet

nstlist = 10

ns-type = Grid

pbc = xyz

periodic-molecules = FALSE

verlet-buffer-tolerance = 0.005

rlist = 1.345

rlistlong = 1.345

nstcalclr = 10

coulombtype = PME

coulomb-modifier = Potential-shift

rcoulomb-switch = 0

rcoulomb = 1.2

epsilon-r = 1

epsilon-rf = inf

vdw-type = Cut-off

vdw-modifier = Potential-shift

rvdw-switch = 0

rvdw = 1.2

DispCorr = EnerPres

table-extension = 1

fourierspacing = 0.16

fourier-nx = 64

fourier-ny = 64

fourier-nz = 72

pme-order = 4

ewald-rtol = 1e-05

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald-geometry = 0

epsilon-surface = 0

implicit-solvent = No

gb-algorithm = Still

nstgbradii = 1

rgbradii = 1

gb-epsilon-solvent = 80

gb-saltconc = 0

gb-obc-alpha = 1

gb-obc-beta = 0.8

gb-obc-gamma = 4.85

gb-dielectric-offset = 0.009

sa-algorithm = Ace-approximation

sa-surface-tension = 2.05016

tcoupl = V-rescale

nsttcouple = 10

nh-chain-length = 0

print-nose-hoover-chain-variables = FALSE

pcoupl = No

pcoupltype = Isotropic

nstpcouple = -1

tau-p = 1

compressibility (3x3):

compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p (3x3):

ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

refcoord-scaling = No

posres-com (3):

posres-com[0]= 0.00000e+00

posres-com[1]= 0.00000e+00

posres-com[2]= 0.00000e+00

posres-comB (3):

posres-comB[0]= 0.00000e+00

posres-comB[1]= 0.00000e+00

posres-comB[2]= 0.00000e+00

QMMM = FALSE

QMconstraints = 0

QMMMscheme = 0

MMChargeScaleFactor = 1

qm-opts:

ngQM = 0

constraint-algorithm = Lincs

continuation = FALSE

Shake-SOR = FALSE

shake-tol = 0.0001

lincs-order = 4

lincs-iter = 1

lincs-warnangle = 30

nwall = 0

wall-type = 9-3

wall-r-linpot = -1

wall-atomtype[0] = -1

wall-atomtype[1] = -1

wall-density[0] = 0

wall-density[1] = 0

wall-ewald-zfac = 3

pull = FALSE

rotation = FALSE

interactiveMD = FALSE

disre = No

disre-weighting = Conservative

disre-mixed = FALSE

dr-fc = 1000

dr-tau = 0

nstdisreout = 100

orire-fc = 0

orire-tau = 0

nstorireout = 100

free-energy = no

cos-acceleration = 0

deform (3x3):

deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

simulated-tempering = FALSE

E-x:

n = 0

E-xt:

n = 0

E-y:

n = 0

E-yt:

n = 0

E-z:

n = 0

E-zt:

n = 0

swapcoords = no

adress = FALSE

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1 = 0

userreal2 = 0

userreal3 = 0

userreal4 = 0

grpopts:

nrdf: 81349 118038

ref-t: 323 323

tau-t: 0.1 0.1

annealing: No No

annealing-npoints: 0 0

acc: 0 0 0

nfreeze: N N N

energygrp-flags[ 0]: 0

Using 1 MPI process

Using 1 OpenMP thread

Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen

A smooth particle mesh Ewald method

J. Chem. Phys. 103 (1995) pp. 8577-8592

-------- -------- — Thank You — -------- --------

Will do ordinary reciprocal space Ewald sum.

Using a Gaussian width (1/beta) of 0.384195 nm for Ewald

Cut-off’s: NS: 1.345 Coulomb: 1.2 LJ: 1.2

Long Range LJ corr.: 4.2451e-04

System total charge: 0.000

Generated table with 4689 data points for Ewald.

Tabscale = 2000 points/nm

Generated table with 4689 data points for LJ6.

Tabscale = 2000 points/nm

Generated table with 4689 data points for LJ12.

Tabscale = 2000 points/nm

Generated table with 4689 data points for 1-4 COUL.

Tabscale = 2000 points/nm

Generated table with 4689 data points for 1-4 LJ6.

Tabscale = 2000 points/nm

Generated table with 4689 data points for 1-4 LJ12.

Tabscale = 2000 points/nm

Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald -1.000e-05

Thanks in advance !