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

[Justin A. Lemkul]

Arik Cohen wrote:
> 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.
> 

If this is just a periodicity artifact, fix it with trjconv.

-Justin

> 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"); 
>>>

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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