[gmx-developers] pull code generalization feedback request

XAvier Periole x.periole at rug.nl
Mon Oct 21 14:20:41 CEST 2013


I realise that this is a bit late but it would be really great to be able to include multi-dimensional umbrella sampling with the option to define multiple bonds, angles and dihedrals simultaneously. 

We use "routinely" the definition of one bond, two angles and three dihedrals to control the relative orientation of two objects (mainly proteins). The retraction of the orientation reduce enormously the sampling to perform to explore interfaces … 

Until now we used particle decomposition to be able to scale over processors. The bonded terms become quickly a limitation in the decomposition of the system. You are probably aware of the recent problems PD has been associated with. The definition of these variables through the "pull" code would be a great replacement :))


On Sep 30, 2013, at 12:45 PM, Berk Hess <hess at kth.se> wrote:

> Hi,
> The pull code in Gromacs, although widely used, has always been somewhat restricted in features and the interface is a little awkward. I want to improve this for 5.0. But to avoid bugs as much as possible and to keep the interface understandable, I would like to limit the features to the minimum. I don't know what people would like to use the pull code for, so I need some feedback on what people might want.
> I have created a redmine feature request and listed there what the minimum is I want to add, as well as my suggestion for a new mdp option layout. Please add you comments in redmine.
> Cheers,
> Berk
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list