Dear gromacs Users,<br><br>I found this in the web, but I wanted to know if there exists the possibility now of using implicit solvent efficiently.<br><br>Thanks,<br>Esteban<br><br><p>A repeating question on the mailing list whether GROMACS can perform <span style="background-color: yellow;"><span>implicit</span></span> <span style="background-color: yellow;"><span>solvent</span></span>
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.).</p>
<ul><li> R. Zhou and B. J. Berne. <i>Can a continuum <span style="background-color: yellow;"><span>solvent</span></span> model reproduce the free energy landscape of a â-hairpin in water?</i>, Proc. Natl. Acad. Sci. U.S.A. 99 (2002), 12777-12782 <a title="dx.doi.org/10.1073/pnas.142430099" rel="external nofollow" href="http://dx.doi.org/10.1073/pnas.142430099" target="_blank">DOI</a></li>
<li> Young Min Rhee, Eric J. Sorin, Guha Jayachandran, Erik Lindahl, and Vijay S. Pande. <i>Simulations of the role of water in the protein- folding mechanism</i>, Proc. Natl. Acad. Sci. U.S.A. 101 (2004), 6456-6461 <a title="dx.doi.org/10.1073/pnas.0307898101" rel="external nofollow" href="http://dx.doi.org/10.1073/pnas.0307898101" target="_blank">DOI</a></li>
<li>
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 <a title="dx.doi.org/10.1073/pnas.0408857102" rel="external nofollow" href="http://dx.doi.org/10.1073/pnas.0408857102" target="_blank">DOI</a></li></ul>
<p> 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.</p>
<p> 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.</p>
<p> There are some tricks we can use (e.g. only calculating surface every N steps), but we still need a <b>very</b>
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.</p>
<p> 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 (<a rel="external nofollow" href="mailto:lindahl@cbr.su.se" title="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>) have reference code that calculates both surface/volume and the associated derivatives analytically.</p>
<br>