[gmx-developers] Marto Carle routine for Gromacs

René Pool r.pool at few.vu.nl
Wed Sep 29 15:49:43 CEST 2010

Yep, that's me!
Sorry for not keeping you posted.
As of yet I have not started implementing GCMC in gromacs. I'm opting 
using a python shell that calls the gmx libraries to get the necessary 
information for performing CGMC moves. I'm planning to start coding with 
in a week or two.

I will report to this list if I make any progress!


René Pool
IBIVU/Bioinformatics, Vrije Universiteit Amsterdam
De Boelelaan 1081a, 1081HV AMSTERDAM, the Netherlands
Room P120
E: r.pool at few.vu.nl
T: +31 20 59 83714
F: +31 20 59 87653

André Assunção S. T. Ribeiro wrote:
> Well, the algorithm as it is can do simple moves (rigid body or bond 
> stretching, bond angle/dihedral angle bending) on NVT and NPT. For the 
> last couple of months I've been working on the implementation of 
> concerted moves in order to simulate peptides. I've been implementing 
> the concerted angle approach of Ulmschneider & Jorgensen (JCP 2003) and 
> trying to make the algorithm satisfy detailed balance, with no luck yet. 
> Some time ago someone contacted me interested in implementing GCMC, but 
> I never heard from him again.
> cheers,
> Andre.
> 2010/9/27 André Assunção S. T. Ribeiro <aastr at yahoo.com.br 
> <mailto:aastr at yahoo.com.br>>:
>  > Yes, I've been working on it. Feel free to contact me if you want to 
> discuss
>  > the status of the implementation or want to cooperate.
> I would be interested in the status here, and would be willing to help
> the effort as I can. I've done some work with established monte carlo
> integrators, enabling the use of modern all-atom forcefields such that
> things like chirality inversion in proteins, cold fusion, etc., are
> properly treated. Though, I have little experience with the Gromacs
> source (especially v. 4).
> All the best,
> Anthony
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