[gmx-users] confusion about implicint solvent
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 23 22:28:14 CEST 2013
On 2013-09-23 20:23, Justin Lemkul wrote:
> On 9/23/13 2:08 PM, Szilárd Páll wrote:
>> Admittedly, both the documentation on these features and the
>> communication on the known issues with these aspects of GROMACS has
>> been lacking.
>> Here's a brief summary/explanation:
>> - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu
>> which is essentially mdrun + OpenMM, hence it has some limitations,
>> most notably it can only run on a single GPU. The performance,
>> depending on setting, can be up to 10x higher than on the CPU.
>> - GROMACS 4.6: the native GPU acceleration does supports only explicit
>> solvent, mdrun + OpenMM is still available (exactly for implicit
>> solvent runs), but has been moved to the "contrib" section which means
>> that it is not fully supported. Moreover, OpenMM support - unless
>> somebody volunteers for maintenance of the mdrun-OpenMM interface -
>> will be dropped in the next release.
>> I can't comment much on the implicit solvent code on the CPU side
>> other than the fact that there have been issues which AFAIK limit the
>> parallelization to a rather small number of cores, hence the
>> achievable performance is also limited. I hope others can clarify this
> I never got the implicit code to run on more than 2 CPUs, and as I
> recall Berk hard-coded this due to a limitation involving constraints.
> It's been a couple years since I tried anything with implicit since (1)
> the OpenMM support was so buggy and incomplete on GPU and (2) the code
> ran an order of magnitude slower on CPU than the explicit solvent
And finally, even though this is not what you were asking, and likely
not wanted to hear either: with implicit solvent your results will not
be general enough to be useful, if e.g. hydrogen bonds are important. I
would like to recommend my latest paper which shows how solvent entropy
and enthalpy contribute in a complex manner to non-bonded interactions
in a way that implicit solvent never could:
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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