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

[Mark Abraham]

Sounds to me like the model is broken, if you can only observe sensible
things in the presence of heat to flow between cations and anions via the
thermal reservoir. Does NVE work?

Mark


On Thu, Jul 24, 2014 at 10:27 PM, Brian Yoo <Brian.S.Yoo.12 at nd.edu> wrote:

> 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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