[gmx-users] IMPLICIT SOLVENT IN AMBER

[Per Larsson]

Hi!

Starting an implicit solvent simulation works just as starting a "normal", explicit solvent simulation, except there is no solvent molecules.
You should use version 4.5.3 for this though (4.0.5 will not work). 

Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx, grompp, mdrun etc... as you otherwise would do.
The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC} and the non-polar solvation is calculated using sa_algorithm=Ace-approximation.

Cheers
/Per

10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:

> 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 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
> 
> -- 
> Sincerely,
> Yulian Gavrilov
> 
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