GROMACS version: 5.1.2
GROMACS modification: Yes/No
Here post your question
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 !