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

[Mark Abraham]

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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