Folding Forum

GROMACS (http://www.gromacs.org/) has release their newest GROMACS 4.0 RC1 on 9/22/2008.
Will FAH follow their step?Will you adopt new edition`s advantages ?

lol I'm still waiting for Gromacs 33 core on PPC which I assume will never see the light of day.

The answer is yes, if it will be beneficial to their research. However it takes some time for new cores to be created and as such if it would be beneficial don't expect to see a hypothetical Gromacs 40 core before next year, assuming they decide to start coding now...

I also expect that if they do want to create a core based on Gromacs 4.0 they will wait until it is in its finished form, rather then being a release candidate...

So when the cores are updated, this will be beneficial to all folding platforms? single CPU, SMP, GPU & PS3?

We use different versions of Gromacs in different cores. Several cores have our own scientific enhancements, many of which are currently being integrated into future Gromacs versions. The A2 core uses a version of Gromacs very close to 4.0RC1.

The latest version of Gromacs from http://www.gromacs.org/ is 4.0, the one that FaH is using is 1.90. Will the core be updated any time soon? If not, why?

For an official answer, you'll need to hear it from the Pande Group.

Generally speaking, there's a fair amount of work to port the gromacs code to a FahCore. The Pande Group also makes code improvements over time which are probably, but not necessarily, incorporated into later versions of Gromacs. You'll notice that there are quite a number of Gromacs variants used on selected projects, already.

As to how soon a new version might be ported, it depends on two factors -- how important the new features in new version are compared to whatever else is in development, and how much programming time is required to port it and to validate those improvements.

You'll notice that Gromacs 3.3 is available, so they're not stuck with 1.90, as you suggest. Nevertheless, there's no point in stopping using an old version if it's giving accurate results, just because there's a new version out.

It's very likely that there's already a 4.0 project underway, but you probably won't get any real details until it's ready to go.

FYI the core version numbers have no relationship with the version of GROMACS being used in the core. All the current cores are based on at least GROMACS 3, with others being based on version 3.3 or development code straight from the source repository.

Thanks everyone. This is the version number that I was on about.

[15:35:10] Folding@Home Gromacs Core
[15:35:10] Version 1.90 (March 8, 2006)

The Gromacs's source doesn't seem to have a lot of changes over time. (http://www.gromacs.org/content/view/79/98/) I think the core is fairly new.

fangfufu wrote:Thanks everyone. This is the version number that I was on about.

[15:35:10] Folding@Home Gromacs Core
[15:35:10] Version 1.90 (March 8, 2006)

The Gromacs's source doesn't seem to have a lot of changes over time. (http://www.gromacs.org/content/view/79/98/) I think the core is fairly new.

Yes, that's the version of the core, not the version of GROMACS.

Yes, while core 78 is older, new Gromacs finds its way in new cores (the A_ series is a good example). Note that it's important for production calculations to have cores that are stable, so we will often put new code into a new core version and then stabilize that version when all is well and move on to a new one.

The A0 uniprocessor core is based on Gromacs 3.3 ... and I think it's the same for A1 and A2 SMP cores.

Thanks everyone for the answer. It is interesting to see this post attracted attention from the senior members of the forum.

toTOW wrote:The A0 uniprocessor core is based on Gromacs 3.3 ... and I think it's the same for A1 and A2 SMP cores.

From what I've read on the forum about the problem with the A2 core for windows being that they're having trouble getting Gromacs 4 to compile on Windows, I think at least that core is based on Gromacs 4.0.

When I read about this, the A2 core was based on a pre-release version of Gromacs 4 ... we might call it "3.3.99" for instance

We don't know (yet) whether v4 compiles better on Windows or not ...