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

[Mark Abraham]

Arik Cohen wrote:
> Hi,
> 
> Thanks for answering so quickly !. Apparently whole residues have 
> detached from the protein.

So... like I asked last time, are you seeing a periodicity artefact? 
"Detached" covers a whole gamut of possibilities.

> 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.

If you've got atoms duplicated, then it sounds like something's going 
wrong with how they're interpreting the structure file, or how you're 
manipulating it afterwards. Either way, it's not a problem for the 
GROMACS mailing list unless you can demonstrate the atoms are duplicated 
in the structure file (which they aren't!).

Mark

> 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"); 
>