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.
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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