Hi Erik, That statement was a typo. The simulation will be done in implicit solvent ( not in gas phase). Sanku
________________________________ From: Erik Marklund <er...@xray.bmc.uu.se> To: Sanku M <msank...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, January 11, 2013 5:04 AM Subject: Re: [gmx-users] mdp option for implicit solvent simulation Hi, If you're simulating in the gas-phase, how come you want implicit solvent? Erik On Jan 11, 2013, at 5:07 AM, Sanku M wrote: > 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 -- 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
