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Hi,<br>
<br>
Sorry to bother you again ,but its not only a periodic effect since
only <b>some of the atoms</b> 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.<br>
In addition, the "detached" group includes three segments of the
protein(8 residues(126-131), 8 residues(157-164) and 4 residues186-189).<br>
<br>
Thanks a lot<br>
<br>
Arik <br>
<br>
Justin A. Lemkul wrote:
<blockquote cite="mid:4B3D0244.9070003@vt.edu" type="cite"><br>
<br>
Arik Cohen wrote:
<br>
<blockquote type="cite">Hi,
<br>
<br>
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.
<br>
In addition,
<br>
I would appreciate as before any suggestion you might have in the
matter.
<br>
<br>
</blockquote>
<br>
If this is just a periodicity artifact, fix it with trjconv.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Thanks
<br>
<br>
Arik
<br>
<br>
Mark Abraham wrote:
<br>
<blockquote type="cite">Arik Cohen wrote:
<br>
<blockquote type="cite">Hi,
<br>
<br>
Thanks for answering so quickly !. Apparently whole residues have
detached from the protein.
<br>
</blockquote>
<br>
So... like I asked last time, are you seeing a periodicity artefact?
"Detached" covers a whole gamut of possibilities.
<br>
<br>
<blockquote type="cite">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.
<br>
</blockquote>
<br>
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!).
<br>
<br>
Mark
<br>
<br>
<blockquote type="cite">Arik
<br>
<br>
Mark Abraham wrote:
<br>
<blockquote type="cite">Arik Cohen wrote:
<br>
<blockquote type="cite">Dear GROMACS users,
<br>
<br>
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.
<br>
</blockquote>
<br>
"main group" of what? Do the atoms bound to them move also? Are you
seeing a periodicity artefact?
<br>
<br>
Mark
<br>
<br>
<blockquote type="cite">The problem appeared only after
adding salt to the simulation(at least in the case of BPTI).
<br>
I would appreciate any suggestions and comments on the matter.
<br>
<br>
Thanks
<br>
<br>
Arik
<br>
<br>
The run files are:
<br>
<br>
*em.mdp:*
<br>
<br>
title = tmRBP_Unliganded_2FN9 Minimization
<br>
integrator = steep ; (steep)using steepest descent
<br>
nsteps = 50000
<br>
nstlist = 1
<br>
rlist = 1.0
<br>
coulombtype = PME
<br>
rcoulomb = 1.0
<br>
vdw-type = cut-off
<br>
rvdw = 1.0
<br>
nstenergy = 10
<br>
emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
<br>
<br>
<br>
*pr.mdp
<br>
*
<br>
title = tmRBP_Unliganded_2FN9 PR
<br>
integrator = md
<br>
nsteps = 50000
<br>
dt = 0.002 ;(in ps) doing a 100ps traj.
<br>
constraints = all-bonds
<br>
nstlist = 10 ; neighbour list updates every number of
steps
<br>
rlist = 1.0
<br>
coulombtype = PME
<br>
rcoulomb = 1.0
<br>
vdw-type = cut-off
<br>
rvdw = 1.0
<br>
tcoupl = Berendsen
<br>
tc-grps = Protein non-protein
<br>
tau-t = 0.1 0.1
<br>
ref-t = 298 298
<br>
Pcoupl = Berendsen
<br>
tau-p = 1.0
<br>
compressibility = 5e-5 5e-5 5e-5 0 0 0
<br>
ref-p = 1.0
<br>
nstenergy = 100
<br>
define = -DPOSRES ; include posre.itp(position restraint)
file
<br>
<br>
*run.md
<br>
*title = tmRBP_Unliganded_2FN9
<br>
integrator = md
<br>
nsteps = 300000
<br>
dt = 0.001
<br>
constraints = all-bonds
<br>
nstlist = 10
<br>
rlist = 1.0
<br>
coulombtype = PME
<br>
rcoulomb = 1.0
<br>
vdw-type = cut-off
<br>
rvdw = 1.0
<br>
tcoupl = V-rescale ;V-rescale
<br>
tc-grps = Protein non-protein
<br>
tau-t = 0.8 0.8
<br>
ref-t = 298 298
<br>
nstxout = 1000
<br>
nstvout = 1000
<br>
nstxtcout = 1000
<br>
nstenergy = 1000
<br>
<br>
<br>
<br>
The runs commands are(integrated inside a C++ code):
<br>
<br>
SysCommand1 = "echo 6 | pdb2gmx -f " + FileName + " -water tip3p";
<br>
<br>
system("editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro");
<br>
<br>
system("genbox -cp box.gro -cs spc216.gro -p topol.top -o
solvated.gro");
<br>
<br>
<br>
minimization:
<br>
--------
<br>
if(Mode == "NoSalt")
<br>
{
<br>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
em.tpr");
<br>
<br>
//system("mpirun -np 4 mdrun -v -deffnm em");
<br>
}
<br>
if(Mode == "WithSalt")
<br>
{
<br>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o
em.tpr");
<br>
system("mpirun -np 4 mdrun -v -deffnm em");
<br>
}
<br>
<br>
<br>
Salting:
<br>
--------
<br>
system("echo 12 | genion -s em.tpr -conc 0.1 -neutral -o
solvated.gro");
<br>
<br>
pr:
<br>
----
<br>
system("grompp -f MDP/prmd.mdp -p topol.top -c em.gro -o pr.tpr");
<br>
/* The actual run*/
<br>
system("mpirun -np 4 mdrun -v -deffnm pr"); </blockquote>
</blockquote>
<br>
</blockquote>
</blockquote>
</blockquote>
<br>
</blockquote>
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