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

[Arik Cohen]

Hi,

With regards to your question I do see some periodicity in which for a 
section of time in the trajectory some of the Calphas in the "detached 
group" are vanishing from it and reappear in the main protein.
In addition,
I would appreciate as before any suggestion you might have in the matter.

Thanks

Arik

Mark Abraham wrote:
> 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"); 
>>