[gmx-users] LINCS WARNING
keramati.ma3oud at gmail.com
Mon Dec 7 14:01:57 CET 2015
Hi to all dear gmx users
during the Energy Minimization i got this warning in first few steps
after step 20
"step 20: Water molecule starting at atom 34209 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate."
but after 3021 steps it was converged to Fmax < 1000.
then i start the Equilibration and in the zero to 4 steps i got this:
"Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018591, max 0.374857 (between atoms 2409 and 2411)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length"
in the step 5i got this and mdrun was terminate.
" Water molecule starting at atom 32146 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
WARNING: Listed nonbonded interaction between particles 2312 and 2326
at distance 4211.247 which is larger than the table limit 2.034 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Segmentation fault (core dumped)"
my Equilibration is:
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.135 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = system ; 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
; 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
tnx for your help
More information about the gromacs.org_gmx-users