[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

[Arik Cohen]

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");  
>>