[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Arik Cohen
acohen at biochem.duke.edu
Tue Jan 5 22:05:01 CET 2010
Dear Gromacs users,
In continuation to the problem below, it seems that self interaction is
not the problem since a -d 1.5nm around the protein should have been
more than enough. Not noticing earlier, I see strange files being
created with the name "step1150b_n1.pdb"
(a bug like structural report of that step ?). In those files and in the
pdb created after applying trjconv, the protein is drifted from the
cell's center to one of the edge and a fragment appears at the other side.
Saying that, trjconv does not solves the problem.
I would be most thankful for any comment/suggestion as to how to prevent
this drift which causes in turn to the "fragment" problem.
Thank
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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