Shi, Huilin 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?
Your settings are correct, although epsilon_r and epsilon_rf are unnecessary.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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