GROMACS version: 2020.1
GROMACS modification: No
System: 1 polymer chain (coarse-grained) in 14000 water molecule. This is a 10-mer with each monomer containing constrained rings and some side-chains.
Force-field: MARTINI 3
Fatal error: Too many LINCS warnings (1001)
Simulation design: Initial minimisation followed by a NVT run (500 ps), a short NPT run (dt =0.001, run time=5ps) before starting this NPT production long run.
Image visualization: After visualizing the images, I have found that there is overlapping between beads in the NPT run. Although there’s no overlap in the previous runs (Min, NVT, short NPT), there are beads which are too close. However, I don’t know how to solve this. So need some help.
All these steps have converged before I started this NPT long run which has crashed with this warning. Can you please help?
Long NPT Production run with these mdp set-up:
integrator = md
dt = 0.001
nsteps = 500000 ; 5ns
nstcomm = 100
comm-grps =
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 200
nstenergy = 200
nstxout-compressed = 1000
compressed-x-precision = 1000
compressed-x-grps = System
energygrps = System
cutoff-scheme = Verlet
nstlist = 10
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
coulomb-modifier = Potential-shift-verlet
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
vdwtype = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 298
Pcoupl = parinello-rahman
Pcoupltype = isotropic
tau_p = 12.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 298
gen_seed = 473529
constraints = none
constraint_algorithm = lincs
lincs_order = 8
lincs_iter = 2
lincs_warnangle = 60