[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 31 22:19:17 CET 2009
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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