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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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