GROMACS version:4.5
GROMACS modification: Yes/No
Hi,
I created a slab of MoS2 to investigating the trend of spreading some polar and non-polar solvents on it. I wasn’t successful, because it made an error “your system isn’t well equilibriumed “.
Has anyone had this problem? Would you share with me your experience?
Thank you
Hi Maryam,
It’s a bit hard to help further without further information:
Did you run an energy minimisation before starting the simulation? Do you use temperature or pressure coupling?
On a side note - I notice that the GROMACS version that you are using is very old. This is most likely not the source of your error, but especially when starting a new project, it’s very useful to upgrade to the newest version which will give you much better simulation performance among other things.
Dear cblau,
Yes, I run minimization step before starting simulation.
I want to did it at room temperature at first.
I will test with a new version
Thanks
Beyond upgrading to more modern software, here are a few tips:
- Please provide a more complete description of your system - what is in it (all the different molecules), how you built it, and where you got your force field parameters.
- Have you validated that individual species are stable via energy minimization and short simulations of each component alone?
- Provide all
.mdpfiles you are using. - What was the outcome of energy minimization on the full system (what Fmax did you achieve)?
- Always provide the full, exact error message copied and pasted from your terminal.
- Other generic advice for unstable systems can be found at http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system
Dear Dr. Jastin Lemkul
I want to investigate the spreading of [BMIM][BF4] droplet on the surface of MoS2 slab.therefore I started by introducing the Mo, S atoms to the force field (opls-aa) in 3 folders (atomtypes.atp, ffbonded.itp, and ffnonbonded.itp). Then , I made itp and topology files for it. I followed {https://github.com/orlandoacevedo/IL} for making itp and topology files for ionic liquid.
my mdp file contains :
[title = NVT equilibration for MOS BMI
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 1000000 ; 0.002 * 30000000 = 60000 ps
dt = 0.0015 ; 2 fs
; Output control
nstxout = 10000 ; save coordinates every 0.2 ps
nstvout = 10000 ; save velocities every 0.2 ps
nstenergy = 10000 ; save energies every 0.2 ps
nstlog = 10000 ; update log file every 0.2 ps
nstxtcout = 10000 ; xtc compressed trajectory output every 10 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
;constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.5 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.5 ; short-range electrostatic cutoff (in nm)
rvdw = 1.5 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.25 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = MOS BMI BF ; three coupling groups - more accurate
tau_t = 0.2 0.2 0.2 ; time constant, in ps
ref_t = 298 298 298 ; 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 = 298 ;temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
freezegrps = MOS
freezedim = Y Y Y]
The error command is :
Fatal error:
120 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
Simplify your system. Make sure you can run the ionic liquid on its own, then run the slab on its own. Since you’re freezing something, you may need energygrp_excl as the manual advises.