Thanks again! Don't you know how to make a total charge = 0 in this case, if implicit salt concentration is not implemented currently? Or it is not critically?
2011/3/10 Per Larsson <[email protected]> > Hi! > > Yes, except that in point 2, I'm not sure about the effects of explicit > ions in an implicit solvent. > Do deal with that properly one should use an implicit salt concentration, > but that is not implemented currently. > The choice of water-model with pdb2gmx is not important. You can choose > 'None' here. > > Cheers > /Per > > 10 mar 2011 kl. 10.39 skrev 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 <[email protected]> > >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > Sincerely, > > Yulian Gavrilov > > > -- Sincerely, Yulian Gavrilov
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