[gmx-users] Implicit solvent, Generalized Born ...

[Stéphane Teletchéa]

Dear colleagues,

I've searched through the archives and questions about Generalized born 
models seem quite recurent but without any real answer.

However, when one runs a gromacs simulation (gromacs 3.3 at least), he 
can see in the log file:

########################################################################
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 2
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
########################################################################

I've searched in the code, in mail archives (see below) and in published 
work but it seems the only work related to this implementation has been 
made by Hao Fan, Alan E. Mark, Jiang Zhu, and Barry Honig 
(http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15814616)

I'd like to consider GB as a good choice for molecular dynamics 
simulations, for energy minimisations and for energy comparisons but 
before can we get more input about:

1 - GB activation in Gromacs (input parameters, flags, ...)
2 - support and experience about it.
3 - was this implementation a 'proof of concept' or a complete 
integration into Gromacs ?

Thanks a lot in advance for comments and explanations.
Yours Sincerely,

Stéphane Téletchéa


As far as i've found, here are the files where GB is mentionned :
./gmxlib/nonbonded/nb_kernel/mknb_interactions.c
./gmxlib/nonbonded/nb_kernel/mknb_common.c
./gmxlib/nonbonded/nb_kernel/mknb.c
./gmxlib/names.c
./gmxlib/nrnb.c
./kernel/grompp.c
./kernel/readir.c

Extracted from the archives:
http://www.gromacs.org/pipermail/gmx-users/2004-July/011623.html
http://www.gromacs.org/pipermail/gmx-users/2005-June/016018.html
http://www.gromacs.org/pipermail/gmx-users/2004-October/012596.html
http://www.gromacs.org/pipermail/gmx-developers/2002-June/000233.html


-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901