LINCS Warning + Set Environment variable

User discussions
#1

GROMACS version: 2019.3
GROMACS modification: Yes/No
Here post your question

I am facing this error:

Fatal error:
Too many LINCS warnings (1001). 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.

I tried to modified mdp file little bit based on researchgate notes, but still getting error. Even I don’t have any idea how to set the environment variable.

Would you please look and advise me to get rid off?

Here is my mdp file:
;Lowry et al (2016) – Novel Dispersant for Formation Damage Prevention in CO2: A Molecular Study –
title = OPLS Asp-CO2 MD equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 40000000 ; 2 * 40000000 = 80000 ps (80 ns)
dt = 0.002 ; 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 = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
energygrps = ANO CO2
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 100 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = System ; coupling groups
tau_t = 2.0 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = parrinello-rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 4.0 ; 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

#2

Looks like you’re using non-standard species. Have you verified that their topologies are sensible? Does the simulation run without any non-standard molecules?

#3

I want to study this article: https://pubs.acs.org/doi/10.1021/acs.energyfuels.6b01512

From this, I used ANO asphaltene and taking CO2 as a precipitant. Here are my working documents:

Thank you.

#4

If you’re trying to reproduce a published study, I suggest contacting the corresponding author and asking for example inputs.

#5

Yes, I asked them. No response yet.

One more interesting thing is - one of my simulation (MD analysis done) working well with asphaltene structure (O-group from Lowry et al 2017).

But, asphaltene structure (ANO - from Lowry et al 2016: https://pubs.acs.org/doi/10.1021/acs.energyfuels.6b01512) is not working.

Would you please tell me why these structures make different results? CO2 was common precipitant for both cases.

Thank you