Yulian Gavrilov zzeppelin87 at gmail.com
Thu Mar 10 10:10:55 CET 2011

Dear, all
I just begin to work in gromacs.
I would like to run on a protein with amber99.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).

In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
How to change this parameters correctly?
What changes should be done on the previous steps? I mean, how to start a
simulation with implicit solvent model from the very beginning?
Sorry for primitive question, but I did not found any useful information
about it for the begginers.

implicit_solvent         = No

; 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
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension       = 2.092



Yulian Gavrilov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110310/41d8c145/attachment.html>

More information about the gromacs.org_gmx-users mailing list