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

[Brian Yoo]

Thanks for the response.

I have looked at two particles in NVT with v-rescale/large box and there
was nothing wrong with the intra/inter molecular interaction energies. I
also switched rvdw-switch to rvdw without observing any difference.

I ran into a similar issue when using this force field in a system
containing a mixture. I was able to resolve the issue again, though this
time with annealing and varying the temperature coupling groups.

Perhaps this only happens when there are more degrees of freedom and a
greater likelihood for metastability (?).

I will just be a bit more cautious from this point on when running these CG
simulations.

Thanks again,
Brian



On Wed, Jul 23, 2014 at 4:09 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> All sounds very weird. I would be suspicious of the fact that you haven't
> set rvdw. I have no idea what rvdw-switch might do in this context, but I
> definitely think you should verify that systems with just two particles
> have the interaction strength you can compute manually.
>
> Mark
>
>
> On Mon, Jul 21, 2014 at 8:57 PM, Brian Yoo <Brian.S.Yoo.12 at nd.edu> wrote:
>
> > 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
> > exactly.
> >
> > 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
> > liquids.
> >
> > The force field is based on a 9-6 Mie cutoff potential and PME long-range
> > electrostatics.
> >
> > 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
> >
> > ;Electrostatics
> > 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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