[gmx-developers] Marto Carle routine for Gromacs

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Tue Sep 28 00:36:41 CEST 2010

This reminds me about some of the "more coordination" emails that have been
going on.  It seems like there should be "working groups" that are focused
on implementing different features, or different classes of features.

For example, Sander Pronk and I had been doing some independent free energy
calculation improvement, and it took a while to synchronize things once we
started working together.  There are probably a few more people that are
implementing free energy calculations independently, and Sander and I should
be working with them as well.

The more people are working together, the more easily different
functionality can be integrated together, and duplicate work is eliminated.
And the smarter, more general, and cleaner the implementation usually is,
since people have to compromise and compare notes.

Also, programming Gromacs is hard, and it's easy to make mistakes and create
features that don't fit well with the rest of the programs.  If your name
isn't Berk, David, or Erik, odds are the first 2-3 times you implement
something, it won't fit with something in the main Gromacs framework.  And
you have to rewrite it.  Working together minimizes (to some extent) such

There are a number of other things that could probably be grouped together
into working groups, aside from Monte Carlo and free energy methods, based
on this:


For example, Python libraries for gromacs types, integrators, integrated
test sets.

I don't think I have wiki permission, so I can't set this up, but I think it
would be a good idea.  There could possibly be mailing lists for each of
these groups, though I don't know what the extra work entailed in that would
be. Though, I'd be willing to manage, say, a free energy methods working
group, once there was general sign-off and some infrastructure for it on the
web site.  And I'd participate in other working groups (MC, test cases).

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Roland Schulz <roland at utk.edu>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Mon, 27 Sep 2010 18:15:16 -0400
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>,
> "aastr at iq.ufrj.br" <aastr at iq.ufrj.br>
> Subject: Re: [gmx-developers] Marto Carle routine for Gromacs
> Andre is working on it. See:
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo
> <http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo>See also
> the gmx-developers archive for mails from Andre discussing MC.
> On Mon, Sep 27, 2010 at 6:04 PM, Mark Abraham
> <mark.abraham at anu.edu.au<mailto:mark.abraham at anu.edu.au>> wrote:
> ----- Original Message -----
> From: Haiqing Zhao <haizhao at mtu.edu<mailto:haizhao at mtu.edu>>
> Date: Monday, September 27, 2010 13:45
> Subject: [gmx-developers] Marto Carle routine for Gromacs
> To: gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>
>> Hi,everyone,
>> Very nice to join in this team. My name is Haiqing Zhao. And i'm
>> now a Ph.D student of Michigan Technological University. I now
>> have one question about Marto Carle routine for Gromacs. Could
>> you provide me some recent progress about that?
> I'm not aware that there's ever been any work on MC in GROMACS.
> Mark
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