[gmx-users] IMPLICIT SOLVENT IN AMBER

[Yulian Gavrilov]

Thanks!

If I understand you correctly, I need to do this (?):

   1.

   pdb2gmx
   2.

   Adding ions (if I have no SOL, what is better to choose on this step?)
   3.

   Minimization with mdp file, that includes these lines:

   implicit_solvent = GBSA

   gb_algorithm = {Still,HCT,OBC}

   sa_algorithm=Ace-approximation
   4.

   Equilibration (nvt, npt) and MD also with these lines in mdp files.



2011/3/10 Per Larsson <per.larsson at sbc.su.se>

> 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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-- 

Sincerely,

Yulian Gavrilov
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