sudheer babu wrote:
Hi all,
my protein contain 59 aminoacid residues and crstal water molecules 103,
The steps i have done are
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...
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
; 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
This is a bad idea - see http://wiki.gromacs.org/index.php/Thermostats
Mark
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