[gmx-developers] implicit solvent free energy
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Fri Aug 30 15:57:38 CEST 2013
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.
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
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.
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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