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

Arik Cohen acohen at biochem.duke.edu
Thu Dec 31 22:27:40 CET 2009


I'm using dodecahedron -d 0.7



Justin A. Lemkul wrote:
>
>
> Arik Cohen wrote:
>> Hi,
>>
>> I have not tried yet to fix it with trjconv which I will . Attached 
>> is a picture with 4 snapshots taken from the simulation. The C-alphas 
>> in question are emphasized with red color.
>>
>
> Is your unit cell sufficiently large?  It looks like the C-alphas 
> indicated are simply crossing the periodic boundary on the "left" of 
> the frame and interacting with the protein molecule in the "right" of 
> the frame, which would indicate to me that the unit cell is too small 
> and you're seeing spurious PBC interactions (i.e., violation of the 
> minimum image convention).
>
> -Justin
>
>> Thanks
>>
>> Arik
>>
>> Justin A. Lemkul wrote:
>>>
>>>
>>> Arik Cohen wrote:
>>>> Hi,
>>>>
>>>> Sorry to bother you again ,but its not only a periodic effect since 
>>>> only *some of the atoms* in the  "Detached" group are vanishing 
>>>> from this group and reappearing in the main protein group. The rest 
>>>> of the atoms are either always in the detached or the main group.
>>>> In addition, the "detached" group includes three segments of the 
>>>> protein(8 residues(126-131), 8 residues(157-164) and 4 
>>>> residues186-189).
>>>>
>>>
>>> From your description, this sounds exactly like a periodicity 
>>> problem - some of the atoms are crossing the periodic boundary and 
>>> are appearing in strange locations.  Have you even tried trjconv to 
>>> fix it?  That would be useful information, as I see that Mark long 
>>> ago also suggested the same sort of fix.
>>>
>>> It is hard for me to envision what you are seeing.  It would be 
>>> enormously helpful if you could post images (screenshots, etc) of 
>>> the problematic structures to get a more expedient resolution.
>>>
>>> -Justin
>>>
>>>> Thanks a lot
>>>>
>>>> Arik
>>>>
>>>> Justin A. Lemkul wrote:
>>>>>
>>>>>
>>>>> 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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