[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 31 22:33:21 CET 2009
Arik Cohen wrote:
> I'm using dodecahedron -d 0.7
>
>
Was that distance specified with respect to both of the protein molecules in the
unit cell? You can check for spurious PBC interactions with g_mindist -pi.
Anyway, I'd be curious to see how you do with trjconv.
-Justin
>
> 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");
>>>>>>>>>
>>>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>
>
--
========================================
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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