GROMACS version: 2020.1
GROMACS modification: No
Hello, i try running and protein-ligand complex simulation, but i got several errors when running MD simulations. I didn’t find this warning on the other ligand but on specific ligand, but my teammates also use same ligand and success. I find some solution in this forum and try to follow it but i can’t figure it out whats the problems on mine. Heres the error:
Step 84098, time 168.196 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 161624336.000000, max 8174421504.000000 (between atoms 5161 and 5183)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4537 4538 90.0 0.1128 0.1311 0.1111
4537 4539 76.5 0.2717 0.1233 0.1111
5161 5183 86.2 1937.3458 899186368.0000 0.1100
5163 5185 90.0 0.1111 0.2220 0.1111
step 84098: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
theres several step that got LINCS warning, but i add one example here.
theres another error when i try to runing again that said:
"Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. "
and its following with some boxes coordinate
and heres my md.mdp file:
title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
; Bond parameters
continuation = yes ; continuing from NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_LIG Water_and_ions ; 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
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; continuing from NPT equilibration
I already tried several times and still no changes. Thank you in advance!