[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Arik Cohen
acohen at biochem.duke.edu
Fri Jan 1 06:01:27 CET 2010
thanks
Arik
Mark James Abraham wrote:
>
> On 01/01/10, *"Justin A. Lemkul" *<jalemkul at vt.edu> 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.
> Indeed. Further, note that the reappearance of a subset of the
> seemingly detached atoms back with the main group is totally normal.
> With domain decomposition in GROMACS 4, such "broken" molecules can be
> written to the trajectory. Judicious use of trjconv fixes the
> appearance of this non-problem.
>
> Mark
>
>>
>> >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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