GROMACS version:
GROMACS modification: Yes/No
Hi, I am running a simulation of protein DNA complex with some modification in the proteins. I used parameterized the residues with ambertools, and incorporated them accordingly with gromacs manual. Did gradual EM till emtol=100, equilibrated considerably and went for production run. After running for some considerable steps the lincs warning appears. Any suggestions will be helpful . The warning is as given below,
Step 141822, time 141.822 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000016 (between atoms 20108 and 20110)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
99 100 78.0 0.0960 0.0960 0.0960
Step 141823, time 141.823 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000016 (between atoms 20818 and 20820)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
99 100 77.6 0.0960 0.0960 0.0960
Step 141824, time 141.824 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000004, max 0.000017 (between atoms 16038 and 16039)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
99 100 77.2 0.0960 0.0960 0.0960
Program: gmx mdrun, version 2022.3
Source file: src/gromacs/mdlib/constr.cpp (line 240)
Fatal error:
Too many LINCS warnings (1000)
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
,
the mdp parameters that i am using are:
title = OPLS Lysozyme NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 10000000 ; 100 ns
dt = 0.001 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 50000 ; save energies every 100.0 ps
nstlog = 50000 ; update log file every 100.0 ps
nstxout-compressed = 50000 ; save compressed coordinates every 100.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter =1 ;
lincs_order =6 ;
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 2.1 ; short-range electrostatic cutoff (in nm)
rvdw = 2.1 ; short-range van der Waals cutoff (in nm)
epsilon_rf =78.0 ;
; Electrostatics
coulombtype = reaction-field ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; 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 on
pcoupl = C-rescale ; Pressure coupling on in 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
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off