[gmx-users] confusion about implicint solvent
fracarb at myopera.com
Wed Sep 25 12:06:53 CEST 2013
Thank you all for the reply, now I'm much less confuse and thank you
David for the paper.
I wanted to try implicit simulations because I need to speed up a bit my
simulations...but I think that now I'll try something else (coarse
On Mon, 23 Sep 2013, at 08:28 PM, David van der Spoel wrote:
> 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:
> 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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Institute of Structural and Molecular Biology
fra.carbone.12 at ucl.ac.uk
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