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.
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");
------------------------------------------------------------------------
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