[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Arik Cohen
acohen at biochem.duke.edu
Fri Dec 25 03:29:23 CET 2009
Hi,
Thanks for answering so quickly !. Apparently whole residues have
detached from the protein. Another strange thing that happens in pyMol
and VMD is that when I select an atom or a residue in the detached group
the selection appears twice: one in the detached group and one in the
main part.
Thanks allot for all your help
Arik
Mark Abraham wrote:
> Arik Cohen wrote:
>> Dear GROMACS users,
>>
>> While running a simple MD simulation with both a small protein such
>> as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm
>> encountering an odd situation in which one (in the case of BPTI) or
>> several Calphas (in the later case) are "detaching them selfs" from
>> the main group.
>
> "main group" of what? Do the atoms bound to them move also? Are you
> seeing a periodicity artefact?
>
> Mark
>
>> The problem appeared only after adding salt to the simulation(at
>> least in the case of BPTI).
>> I would appreciate any suggestions and comments on the matter.
>>
>> Thanks
>>
>> Arik
>>
>> The run files are:
>>
>> *em.mdp:*
>>
>> title = tmRBP_Unliganded_2FN9 Minimization
>> integrator = steep ; (steep)using steepest descent
>> nsteps = 50000
>> nstlist = 1
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdw-type = cut-off
>> rvdw = 1.0
>> nstenergy = 10
>> emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
>>
>>
>> *pr.mdp
>> *
>> title = tmRBP_Unliganded_2FN9 PR
>> integrator = md
>> nsteps = 50000
>> dt = 0.002 ;(in ps) doing a 100ps traj.
>> constraints = all-bonds
>> nstlist = 10 ; neighbour list updates every number of steps
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdw-type = cut-off
>> rvdw = 1.0
>> tcoupl = Berendsen
>> tc-grps = Protein non-protein
>> tau-t = 0.1 0.1
>> ref-t = 298 298
>> Pcoupl = Berendsen
>> tau-p = 1.0
>> compressibility = 5e-5 5e-5 5e-5 0 0 0
>> ref-p = 1.0
>> nstenergy = 100
>> define = -DPOSRES ; include posre.itp(position
>> restraint) file
>>
>> *run.md
>> *title = tmRBP_Unliganded_2FN9
>> integrator = md
>> nsteps = 300000
>> dt = 0.001
>> constraints = all-bonds
>> nstlist = 10
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdw-type = cut-off
>> rvdw = 1.0
>> tcoupl = V-rescale ;V-rescale
>> tc-grps = Protein non-protein
>> tau-t = 0.8 0.8
>> ref-t = 298 298
>> nstxout = 1000
>> nstvout = 1000
>> nstxtcout = 1000
>> nstenergy = 1000
>>
>>
>>
>> The runs commands are(integrated inside a C++ code):
>>
>> SysCommand1 = "echo 6 | pdb2gmx -f " + FileName + " -water tip3p";
>>
>> system("editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro");
>>
>> system("genbox -cp box.gro -cs spc216.gro -p topol.top -o
>> solvated.gro");
>>
>>
>> minimization:
>> --------
>> if(Mode == "NoSalt")
>> {
>> system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
>> em.tpr");
>>
>> //system("mpirun -np 4 mdrun -v -deffnm em");
>> }
>> if(Mode == "WithSalt")
>> {
>> system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
>> em.tpr");
>> system("mpirun -np 4 mdrun -v -deffnm em");
>> }
>>
>>
>> Salting:
>> --------
>> system("echo 12 | genion -s em.tpr -conc 0.1 -neutral -o
>> solvated.gro");
>>
>> pr:
>> ----
>> system("grompp -f MDP/prmd.mdp -p topol.top -c em.gro -o pr.tpr");
>> /* The actual run*/
>> system("mpirun -np 4 mdrun -v -deffnm pr");
>>
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