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.
-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.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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