Hi, I am trying to do implicit solvent simulation for a protein in gas-phase. I have a few questions : 1) should I use sd integrator?
2) should I also use no periodic condition considering continuum dielectric ? 3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no cutoffs were used for implicit solvent simulations. But, again in implicit solvent setup the rgblist should be equal to rlist. Now, if I use rlist=0 ( as all interactions are considered), should I also make rgblist=0? Does it mean the setup was following type: i.e. ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 0 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz, no, xy pbc = no periodic_molecules = no ; nblist cut-off rlist = 0 ; long-range cut-off for switched potentials rlistlong = -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 0 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA ; 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 = 0 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0.150 ; 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 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = -1 Some idea about the implicit solvent setup will be appreciated. Sanku -- 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
