[gmx-users] Re: openmm

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jul 19 00:40:05 CEST 2009

Alan wrote:
> Thanks Justin.
> I could swear I tried what you said... anyway it worked now (2.5 x
> faster), but not with implicit solvent for mdrun-openmm... Trying with
> plain mdrun with the setup for implicit solvent and it seemed to work
> (although I don't know how to interpret this from
> GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: "even though
> this is not available in the standard Gromacs 4")

 From the link I supplied yesterday:

'Neither cutoffs nor periodic boundary conditions are supported.  The 
"coulombtype" and "vdwtype" settings are ignored, as are the various 
cutoff settings.'

So if this still pertains to your version, your attempt to use 
reaction-field was not useful.

> I still would like an example/tutorial that really worked for someone
> with gmx openmm.

You will need to contact the people who wrote it. I am not aware that 
any of them post here.

> In the end, with mdrun-openmm and implicit solvent in the mdp file, I
> got a file md.gro full of "nan     nan".

All I know is what I can read in the README.


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