Steven Neumann wrote:
On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann
<s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>
<mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>__>
wrote:
On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Steven Neumann wrote:
Dear Gmx Users,
My system includes: ions, water, two tubes made of
carbon
atoms, protein.
I would like to run NVT (and then NPT) with position
restarined dynamics of my protein and tubes.
I am wondering whether this approach is good (two
coupling
groups: Protein_Tubes and Water_and_ions??
My thermostat in mdp file:
Temperature coupling is on
tcoupl = V-rescale ;
tc_grps = Protein_Tubes Water_and_ions ; two coupling
groups
tau_t = 0.1 0.1 ; time constant
ref_t = 298 298 ; reference temperature
Please, let me know whether this apporach is ok. How
can I
set tc_grps when I want to add ligand?
I don't know a definitive answer here, so I'll throw out some
ideas and hopefully stimulate some discussion. I create
tc_grps
based on species whose dynamics are intimately linked. For
solvent, that includes water and ions. Are your protein and
tube physically associated?
They are not physically associated but I put my protein as
close as
possible to the tube and I want to run position restrained
dynamics
of my tube and first 4 residues of my protein (stimulating
attached
protein to my tube).
Will you suggest attaching my protein directly to my tube in
this case?
I'm assuming by "attaching" you mean coupling in the same tc_grp? I
wouldn't. This is a complex case (and again, I don't know a true
answer here) - your system has the potential to be highly dynamic.
Say the protein and tube bind, in which case they would (in theory)
be coupled together. Say they never bind, and then if you couple
them together they shouldn't be. You don't know a priori which way
it will go.
No. I mean physically attached. That is why my first 4 resiudes are
closed to the tube and position restrained. The best would be to attach
it physically by sharing one atom. No clue how. My tube is a
representation of the rest of the protein assembly (I am interested in
the influence of charged "residues" represented by ions and non charged
by carbon atoms within my tube - position restrained dynamics the tube)
on my protein. What is more there is another tube above my protein (not
attached) and I am interested also on the influence of those "residues"
of the tube on my protein conformation. In future I want to do Umrella
Sampling pulling my tube above to see free energy difference.
It would have been better to state all of this up front ;)
If you are trying to create a single entity representing the protein and the
tube, then yes, they should be a single tc_grp, and the best approach is to
create a merged [moleculetype] definition with an actual bond between the shared
atoms. Doing so is not trivial, and I have no real quick way to suggest doing
that, other than recreating a topology from pdb2gmx and perhaps making use of
specbond.dat. I'm still not 100% clear on where everything is located.
The other tube (not attached) and solvent/ions/ligands should likely be treated
as separate groups for the purposes of temperature coupling. But again, as
stated, this is a very complicated system and the best methodology for
simulating it is likely not defined terribly well.
-Justin
--
========================================
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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