[gmx-users] Verlet AND tabulated potential

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 8 09:50:43 CEST 2014

On Mon, Jul 7, 2014 at 3:17 PM, Tamas Karpati <tkarpati at gmail.com> wrote:

> Dear all,
> I have trouble creating a FF without bonds explicitely defined,
> only using "nonbonding" forces of the Buckingham (BH) type to keep
> my crystal in one piece. The problem is related to wrong interatomic
> forces on basis of the ASCII-dumped TRR files. So FF works (at
> least functionally), optimization does not.
> Since replacement of BH by an approximate LJ potential succeeded
> I decided to by-pass the built-in BH code by a tabulated potential.
> Unfortunately, GROMACS (versions 4.6.3, 4.6.5, 5.0-beta2 and 5.0)
> wouldn't take my MDP file.
> I kindly ask your help on the subject. The typical error message
> is coming from GROMPP in the forms:
>   1. "With Verlet lists only cut-off and PME LJ interactions are supported"
>   2. "With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported"
> Never mind the LJ statement above as the same appears with BH, as well.
> The forcefield.itp/[default] contains nbfunc=2 and comb-rule=1.
> The connected part of the MDP file is
>   "...
>   cutoff-scheme   = verlet
>   vdwtype = User
>   coulombtype = User
>   ..."
> I seem to be incompatible (in fact new to) GROMACS or User does not
> much like Verlet cut-offs. I'm stuck. If you have any idea or working
> example, please share it. I'v failed locating relevant info on the Internet
> so far.

As the errors suggest, Buckingham interactions are not supported with the
Verlet cut-off scheme (and neither are user tables, yet). The group cut-off
scheme has support for Buckingham interactions, but only in the plain-C
non-SIMD kernels, which are not fast. You can probably do better (ie. get
SIMD) by using a user table there.


Thanks in advance,
>    toma
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