[gmx-developers] implicit solvent free energy
mark.j.abraham at gmail.com
Sat Aug 31 01:48:06 CEST 2013
On Fri, Aug 30, 2013 at 3:57 PM, Shirts, Michael (mrs5pt)
<mrs5pt at eservices.virginia.edu> wrote:
> Hi, guys-
> I think that GB can be useful for many approximate things. I'm happy to
> help interface the free energy part, once the rest is working.
C all-vs-all kernels work. Otherwise, GB requires PD, which is already
slated for removal. I don't imagine there's huge enthusiasm for
implementing GB+DD for the multi-domain case, so the best
non-all-vs-all scenario might be single-domain. Short term probably
single core, maybe OpenMP when someone is prepared to make that
When I rip out PD in a couple of weeks, I will be looking to make
single-core single-domain GB no worse than it is now. Right now, I
don't know how bad that is ;-)
> I agree that parallelization is the biggest issue for long term support. My
> feeling is that single core GB will be pretty straightforward to get working
> again. The question of how useful single core in. One application of
> implicit solvent methods for large systems in general is aggregation and
> encounter processes, since simulating large amounts of water to support 10's
> of small peptides is rather inefficient. These sorts of problems seem like
> they would easier to parallelize.
> For free energies, I would probably recommend that the GB can be combined
> with free energies entirely through charge scaling. This way, there's no
> need to modify the inner loops at all. I can help work through other
That sounds like something Berk said at lunch this week.
> For any hydrophobic component, this can be handled linearly as well in free
> energies -- no need to put any free energy code in the inner loops.
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
>> From: Per Larsson <per.larsson at sbc.su.se>
>> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>> Date: Fri, 30 Aug 2013 15:41:10 +0200
>> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>> Subject: Re: [gmx-developers] implicit solvent free energy
>> 30 aug 2013 kl. 08:44 skrev David van der Spoel:
>>> On 2013-08-30 01:47, David Mobley wrote:
>>>> Dear Devs,
>>>> I wanted to get a sense how many people are interested in getting the
>>>> implicit solvent and free energy codes playing nice together, and how
>>>> likely it is to happen.
>>>> We're very interested in this, as we do a lot of work related to free
>>>> energy methodology. This means in general we are more interested in
>>>> whether something works (and how well it works) given the force field
>>>> parameters than we are in having the solvent model right. In general,
>>>> implicit solvent will run a lot faster, so we could do a lot of our work
>>>> much more quickly if the free energy code would work well with implicit
>>>> solvent (such as generalized Born, etc.). We've also seen enough work on
>>>> implicit solvent free energy calculations elsewhere (and done some
>>>> ourself in AMBER) to be optimistic about the accuracies we could achieve
>>>> for a number of the problems we're interested in.
>>>> In any case:
>>>> - Are other people similarly interested in this?
>>>> - Are there any efforts underway to get the GB code to work properly
>>>> with free energy?
>>>> - What are the problems/obstacles?
>>> First problem is that GB does not work at all anymore in 4.6 and higher
>>> (correct me if I'm wrong). There are some loops missing IIRC. Maybe you could
>>> look into this if you're interested.
>>> Since I am rather skeptical about GB due to its approximate nature I am not
>>> sure that it is worth the trouble. You would have to compute the derivative
>>> of the GB term with respect to the born radius, right? The manual in section
>>> 3.18 is not entirely complete, but that might be tedious and expensive to
>>> compute as well.
>> When I first implemented this into what was then a pre 4.5 version of gromacs,
>> the implementation had everything in there (including calculations of the
>> derivatives with respect to the radius). I haven't been very active in gromacs
>> development lately due to doing other things for my post-doc, but as long as
>> someone hasn't removed any code it ought to still be there.
>> I'd be happy to come back into a more active role in working with this, with
>> the caveat that free-energy calculations is not exactly my area of expertise.
>> On the other hand, I know the GB-code...
>>>> David Mobley
>>>> dmobley at gmail.com <mailto:dmobley at gmail.com>
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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