[gmx-users] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 2 12:36:20 CEST 2014

On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti <
francesco.mambretti at studenti.unimi.it> wrote:

> Dear all, I am a student in Physics at Milan University. For my thesis, I
> should run a simulation of a binary liquid mixture of Argon and Krypton.
> Until now, I have been learning how to use GROMACS (version 5.0.1 and,
> since
> yesterady, 5.0.2) essentials, and my simulations were all based on LJ
> potential, and all was fine.
> Now I want to use a tabulated potential, that is a more detailed potential,
> different in form from LJ, taken from literature.
> I followed the steps of the instructions on GROMACS website
> (
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential
> )
> and the attached pdf, but it doesn't work.
> I ought to use cutoff-scheme = verlet (because the "group" scheme does not
> make sense, because my system has no charge),

VDW-only systems work fine in the group scheme, e.g. with a single atom per
charge group - but you will need to organize your own details for adequate

> but I receive these errors
> from grompp:
> ERROR 1 [file Aziz.mdp]:
>   With Verlet lists only cut-off and PME LJ interactions are supported
> ERROR 2 [file Aziz.mdp]:
>   With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported
> Aziz.mdp is my mdp file, that contains the instructions coulombtype = User
> and vdwtype = User.
> What am I missing?
> Or it is true that GROMACS is not able to use user-defined potentials with
> verlet's cutoff? This would be a serious handicap for this code!
> Am I forced to use charge groups?

For now, yes. There is work in progress to implement user tables for the
Verlet scheme (& GPUs). Some help with alpha-stage testing would be very
welcome! But for that, you might like to have a working group-scheme setup
against which to validate.


> Thanks in advance,
> Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab)
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