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.
Your subject line is totally unrelated to your post. It's rather
frustrating. Please try to fix that in the future.
Also you could have searched for:
protein out of box
and found your answer immediately. Please search in the future before asking.
For your convenience, You can see here:
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
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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