[gmx-users] gas-phase protein simulation
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 30 21:00:03 CET 2011
yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.
On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <huilshi at imail.iu.edu> wrote:
> 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.
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