On 2013-09-23 20:23, Justin Lemkul wrote:
On 9/23/13 2:08 PM, Szilárd Páll wrote:
Hi,
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
aspect.
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
counterpart.
-Justin
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:
http://pubs.acs.org/doi/abs/10.1021/ct400404q
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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