[gmx-users] IMPLICIT SOLVENT IN AMBER
zzeppelin87 at gmail.com
Thu Mar 10 10:10:55 CET 2011
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 ALGORITHM
implicit_solvent = No
; 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
; 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
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