Hongyan Xiao wrote:
Hi, David van der Spoel
I used the periodic boundary conditions. The box
is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is
the em.mdp file.
Then the minimization works correctly. See chapter 3 in the manual.
;
; User xiao
; 2008.9.28 10:23
; Input file
;
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 20000
nstcomm = 1
ns_type = grid
rlist = 0.8
coulombtype = cut-off
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.2
Tcoupl = no
Pcoupl = no
gen_vel = no
Please help me. Thanks again!
H. Y. Xiao
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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