yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well. Toodle pip!
On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <[email protected]> wrote: > Hi, > > I would like to run a gas-phase protein simulation (with charge state of > +8). > I have read this paper : Biochemistry, 2007, 47, 933-945. > > In the method section of vaccum simulation, it is said > "For the remaining parameters, the same settings were used as in the water > simulations, > except that the periodic boundary conditions were turned off and no cutoffs > whatsoever were used." > > I am confused about "no cutoffs whatsoever were used". > Does that mean setting all the cutoffs to be zero? > In the md.mdp file, can I use the following > > "; NEIGHBORSEARCHING PARAMETERS > nstlist = 0 > ns-type = simple > pbc = no > rlist = 0 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = cut-off > rcoulomb = 0 > epsilon_rf = 78 > epsilon_r = 1 > vdw-type = Cut-off > rvdw = 0" > > Do I need to set rcoulomb/rvdw to zero or some other number? > > Thank you. > > > Huilin > -- > 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
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