[gmx-users] problem regarding protein in water simulation
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 14 08:00:11 CET 2008
Jochen Hub wrote:
> 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).
But it should be said that this will lead to slightly poorer energy
conservation, which is not a problem if you use thermostats. In addition
you won't be able to compute the diffusion constant of your protein. It
could even imply (but this is wild speculation from my side) an
artificial stabilization against unfolding.
> Check also:
> 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,
>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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