[gmx-users] Issues using tabulated potentials for coarse-grained simulation

Brian Yoo Brian.S.Yoo.12 at nd.edu
Mon Jul 21 20:57:31 CEST 2014

Dear gmx-users,

I am running into an issue regarding the use of tabulated potentials for
coarse-grained simulations. My system consists of 256 ion pairs (ionic
liquid) and the simulation is run in the NPT ensemble.

When I use a temperature coupling on the system as a whole, my system ends
up freezing such that the ions vibrate in position. The temperatures and
pressures are correct, but the density is much higher than what it should
be. Also, the system is stable and the simulation runs indefinitely.
However, if I set temperature coupling of anions and cations separately, my
molecules no longer freeze and I obtain the targeted properties almost

This occurrence is insensitive to varying tau-t's (0.5 to 5.0) or
thermostat (Berendsen or Nose-Hoover), and annealing. It also occurs for
other systems using a similar ionic liquid force field, although I was able
to resolve the issue again by changing the temperature coupling to anions
and cations separately.

I have not run into this type of issue for all atom simulations of ionic

The force field is based on a 9-6 Mie cutoff potential and PME long-range

Has anyone run into a similar issue using tabulated potentials?

Thank you,

Brian Yoo

The mdp parameters are as follows:

integrator      = md
dt              = 0.004
nsteps          = 5000000
comm-mode       = linear
nstcomm         = 1

; Output control
nstxout         = 5000
nstvout         = 5000
nstlog          = 5000
nstenergy       = 5000
nstxtcout       = 5000

; Neighbor searching
nstlist         = 10
ns_type         = grid
pbc             = xyz
rlist           = 1.5

coulombtype     = PME
rcoulomb        = 1.5
fourierspacing  = 0.10
optimize_fft    = yes

; VdW
vdwtype         = user
rvdw-switch      = 1.5

; Temperature coupling
tcoupl          = Berendsen
tc-grps         = C4M PF; System
tau_t           = 0.5 0.5
ref_t           = 300 300

; Pressure coupling
pcoupl          = Berendsen
pcoupltype      = isotropic
ref_p           = 1.0
tau_p           = 3.0
compressibility = 4.5e-5

; Velocity generation
gen_vel         = yes
continuation    = no

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