On 05/07/10 16:27, Justin A. Lemkul wrote:
ithu wrote:
Dear gromacs Users,
I found this in the web, but I wanted to know if there exists the
possibility now of using implicit solvent efficiently.
Implicit solvent will be supported in the upcoming release.
Since it interests me too... How far is the upcoming release from being
useful for general work? That is, is it just unstable but can I *trust*
it in terms of results correctness or it is better to leave it to
developers.
Because in the first case I'd like to try it sooner or later :)
M.
-Justin
Thanks,
Esteban
A repeating question on the mailing list whether GROMACS can perform
implicit solvent simulations. The answer is, not really. Over the last
few years there have been quite a few papers in (good) journals about
why one in general should or should not use it. Please search
literature by Ruhong Zhou, Vijay Pande and/or Bruce Berne on the
subject (and fill in the references here plus DOI links etc.).
* R. Zhou and B. J. Berne. /Can a continuum solvent model reproduce
the free energy landscape of a β-hairpin in water?/, Proc. Natl.
Acad. Sci. U.S.A. 99 (2002), 12777-12782 DOI
<http://dx.doi.org/10.1073/pnas.142430099>
* Young Min Rhee, Eric J. Sorin, Guha Jayachandran, Erik Lindahl,
and Vijay S. Pande. /Simulations of the role of water in the
protein- folding mechanism/, Proc. Natl. Acad. Sci. U.S.A. 101
(2004), 6456-6461 DOI <http://dx.doi.org/10.1073/pnas.0307898101>
* Hao Fan, Alan E. Mark, Jiang Zhu, and Barry Honig. Comparative
study of generalized Born models: protein dynamics, Proc. Natl.
Acad. Sci. U.S.A. 102 (2005), 6760-6764 DOI
<http://dx.doi.org/10.1073/pnas.0408857102>
The current state in Gromacs is that we already have very optimized
assembly kernels for the actual generalized born interaction, so that
part is done. We also have C language functions to calculate Still
radii (not yet in CVS), although these have to be ported to assembly
for decent performance.
The one big remaining issue is a fast surface calculation algorithm.
The problem with the commonly used ones (e.g. Still) is that
everything else in Gromacs (including the GB loops) is an order of
magnitude faster, so that surface calculation would take over 90% of
the time. They also do not parallelize easily.
There are some tricks we can use (e.g. only calculating surface every
N steps), but we still need a *very* fast surface calculation
algorithm. The best starting point in the literature is probably the
algorithm of Brooks, where you simply have empiric parameters for
sp2/sp3/sp neighbors of different atom types combined with a short
neighborlist.
We definitely need approximate derivatives of the surface free energy
with respect to all atom coordinates, and the last couple of years
there has also been some discussion that the volume term could be even
more important than the surface, so preferably volume derivatives too.
If you're interested in helping I (lind...@cbr.su.se
<mailto:lind...@cbr.su.se>) have reference code that calculates both
surface/volume and the associated derivatives analytically.
--
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