[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 31 22:42:55 CET 2009
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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