[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Arik Cohen
acohen at biochem.duke.edu
Thu Dec 31 22:52:04 CET 2009
No, sorry for the confusion. The images are only from a simulation of
one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI was
a bit different in a way that only 1 C-alpha was "detached" (cell size ?).
Arik
Justin A. Lemkul wrote:
>
>
> Arik Cohen wrote:
>> Which two proteins ? I have at least in beginning only one protein
>> which some how is divided into two along the calculation.
>> Any way I'll try both increasing the cell and fix it with trjconv.
>>
>
> Quoting your original message:
>
> "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 assumed that what I was seeing in the images was a set of two
> proteins. My concern was that you defined a box relative to the
> larger protein, then inserted the smaller one (BPTI?), leaving
> insufficient space in the box to satisfy the minimum image
> convention. If that's not what we're looking at, then that'd be
> useful to know :)
>
> If you have a single protein, "divided into two" then the problem is
> almost certainly a simple periodicity artifact. Bonds do not break in
> a normal MD calculation (in fact they can't using the standard MM
> approximations).
>
> -Justin
>
>> Thanks a lot
>>
>> Arik
>>
>> Justin A. Lemkul wrote:
>>>
>>>
>>> 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");
>>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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