Li Qiang wrote:
Dear Gromacs Users,
I wonder if it is normal for a protein to move out of the box during MD
runs. periodic boundary conditions are applied. system is neutralized.
0.9nm for the distance between box side and protein.
first,please use a relevant mail subject.
second the answer is yes. See http://wiki.gromacs.org.
thanks
the md.mdp for your reference:
title = trp-Cage
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.002 ; ps !
nsteps = 2500000 ; total 5000 ps.
nstcomm = 1
nstxout = 500 ; collect data every 1 ps
nstvout = 0
nstfout = 0
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1
tc_grps = system
ref_t = 498
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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