[Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]
Justin A. Lemkul
jalemkul at vt.edu
Tue Jan 5 22:09:22 CET 2010
Arik Cohen wrote:
> 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.
>
Check your log file for LINCS warnings, etc. These step_*.pdb files are written
when the system becomes unstable and is on the verge of collapse. Your system
is probably blowing up, hence the weird coordinates.
-Justin
> 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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--
========================================
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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