[gmx-users] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
francesco.mambretti at studenti.unimi.it
Thu Oct 2 13:13:45 CEST 2014
So then, you have to update the pages on your website (http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) about tabulated potentials, and also in the user manual (5.0.1 version).
Otherwise, people risks misleading about this topic!
In fact, I spent my last month in learning GROMACS, encouraged by the documentation about tabulated potentials (it seems so easy to do that!), and nothing is said about the cutoff scheme you have to use! And also the attached pdf should be updated.
This is a very strong limit, LJ and Buckingham potentials are often not so accurate potentials, if you really want to simulate physical systems.
So the alternatives I have are:
1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each of them is a group charge) and group cutoff - but the run will require more time
2) downgrade my GROMACS version, so that I am not forced to use verlet cutoff if I want a configuration that scales fast
3) use LJ potential
Am I right?
Il 02/10/14, Mark Abraham <mark.j.abraham at gmail.com> ha scritto:
> 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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