[gmx-users] problem regarding protein in water simulation

[Jochen Hub]

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
************************************************