[gmx-users] Using Charmm FF with implicit solvent on gromacs
per.larsson at sbc.su.se
Fri Nov 19 10:10:39 CET 2010
Currently it is not possible to use GBSW in Gromacs.
As you noted, there are three GB-models available (Still,HCT,OBC),
that can be run using plain cutoffs (or no cutoffs at all, using the optimized all-vs-all kernels).
Currently there is unfortunately no work being done to extend the range of implicit solvent models available.
However, we have had some promising results with the combination of CHARMM FF + CMAP + OBC, as discussed in the 2010 JCTC paper.
18 nov 2010 kl. 22.49 skrev César Ávila:
> Dear all,
> I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models
> Hawkins-Cramer-Truhlar (HCT)
> Onufriev-Bashford-Case (OBC)
> The charmm FF has been extensively tested with the GBSW* implementation (in Charmm program) for which the backbone phi/psi cross-term (CMAP) and the atomic input radii were specifically optimized (Chan, Im and Brooks, JACS, 2006).
> Is there a way to perform the same calculation on gromacs?
> * W. Im, M.S. Lee, and C.L. Brooks III "Generalized Born Model with a Simple Smoothing Function." J. Comput. Chem. 24:1691-1702 (2003).
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