>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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