[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 31 22:56:49 CET 2009
Arik Cohen wrote:
> 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 ?).
>
If there is supposed to be only a single protein in the images you've shown (and
after having a look at the 2FN9 structure from the PDB), it seems pretty clear
to me that part of your protein has simply crossed a periodic boundary and
trjconv -pbc mol (or some such command) should fix it.
-Justin
> 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");
>>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
--
========================================
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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