[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Arik Cohen
acohen at biochem.duke.edu
Thu Dec 31 23:07:55 CET 2009
Again Thanks a lot
Arik
Justin A. Lemkul wrote:
>
>
> 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");
>>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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