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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