[gmx-users] gas-phase protein simulation
huilshi at imail.iu.edu
Wed Nov 30 20:39:38 CET 2011
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users