[gmx-users] problem regarding protein in water simulation

[Mark Abraham]

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