Generally there is nothing wrong when the protein diffuses across the
periodic boundaries. However, it is convenient to avoid this by using
comm-grps = Protein
in you mdp file (default (in your simulation) is the whole system
including the water).
Check also:
http://www.gromacs.org/documentation/reference_3.3/online/mdp_opt.html
Cheers, Jochen
sudheer babu wrote:
Hi all,
my protein contain 59 aminoacid residues and crstal water molecules 103,
The steps i have done are co
1.minimisation of protein invacuo
2.added simulation box of 6 in xyz dimensions
3.added water
4.added ions
5.energy minimisation in water
6.positoin restrain in water
7.production step......
My sytem is fine till 250 ps production , after that protein is coming
to outside from water box,
whats the problem ?
have i done any mistake while doing steps or any mistake in md.mdp file
pls help me...
along with my mail, md.mdp file is attaching here,
_md.mdp_
title = dpt_prod
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 125000 ; total 250 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
pbc = xyz
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tc-grps = Protein Sol CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; isotropic pressure coupling is now on
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Energy monitoring
energygrps = Protein Sol CL-
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300
gen_seed = 173529
39,1 Bot
Thanks in advance.
------------------------------------------------------------------------
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--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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