On 28/07/2012 3:01 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
my problem is, that during the md run the atoms are not frozen somehow.
During the minimization run everything worked out fine. But when I did a
md run the hydrogen atoms and the other atoms seems to be changes somehow.
I calculated the RMSD value and this is why I know that they change.
After the minimization the RMSD value between the structure before and
after the minimization was about 9.9515e-08 but after the md run the RMSD
value was 0.000539742 nm which definitely shows that something was
changed.
And I want to now why that happened. Because I thought that with the
freeze option the atoms which are frozen are not changed.
The most likely explanations are that you aren't comparing
configurations that should be the same, or that you are comparing them
over a different set of atoms than were frozen. But without seeing the
commands and groups chosen in your workflow, nobody can know.
Mark
Thank you
I want to do a minimization and a md run with my protein. But I only
want
the hydrogen atoms to be minimized but not the rest of the protein.
I use the
freezegrps = Protein-H
freezedim = Y Y Y
option in my mdp files to make sure that they don't change.
During the minimization steps everything works fine and it really does
not
change.
But now I started the md run and here the protein somehow get minimized
too. I do not understand why everything works fine during the
minimization
but not during the md run.
My mdp file for the md run looks like this:
define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 500
nstenergy = 5
energygrps = Protein Non-Protein
nstcalcenergy = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
gen_vel = yes
gen_temp = 200.0
gen_seed = 9999
constraints = all-bonds
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 298 298
pcoupl = no
freezegrps = Protein-H
freezedim = Y Y Y
Eva -
Sorry, I did not get your question.
But now I started the md run and here the protein somehow get minimized
too. I do not understand why everything works fine during the
minimization
but not during the md run.
Your MDP file should freeze all the atoms in the "Protein-H" index
group. Are these atoms actually non-frozen during MD but frozen during
geometry optimization at zero-T?
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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