[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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