You've basically got the idea. As a subtle point, the "strength" of a method is
completely user-defined (by the tau_p parameter, how frequently the temperature
is coupled). No one method is "stronger" than another, but it is correct to say
that the Nose-Hoover thermostat produces a rigorous NVT ensemble. When used
with Parrinello-Rahman for pressure control, a rigorous NPT ensemble is produced.
If I remember our discussion correctly, you want to fix one end of the molecule
and pull on the other, correct? If so, your pull_group0 will be the residue at
one end of the protein (N- or C-terminus, depending on how you set it up), and
pull_group1 will be the other terminus.
-Justin
Ravi Kappiyoor wrote:
Thank you, Justin. To make sure I understood correctly, you use weak
coupling methods during equilibration (such as V-rescale and Berendsen)
in order to try and avoid large fluctuations. However, during actual MD
simulations, you would recommend using stronger coupling methods such as
Nose-Hoover, correct? Also, one question I forgot to ask in the last
e-mail, in the umbrella sampling, I believe you used the pull command to
pull chain A of the amyloid fibril with respect to chain B. In my case,
I will be testing a single chain of resilin, so how would I adapt this
segment?
On Wed, Aug 4, 2010 at 6:45 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Hi Ravi,
Your questions raise a number of interesting points, most of which
take a few years of experience to fully appreciate :) I will try to
give you a short take on the whole idea of equilibration, as best as
email will allow. I will note, though, that to fully address the
subtleties of what you're asking, it takes quite a lot of textbook
reading. I can recommend a few to you, if you like. We devoted
several weeks to this type of discussion in the class we taught.
The initial equilibration of any system should be approached gently.
Solvent that is added has a very regular, almost crystalline,
configuration. It is very unnatural. NVT equilibration is
typically done before NPT, although I happen to know that the
amyloid fibrils are incredibly resilient and do not require NVT
equilibration. This is only something I happen to have figured out
after a few years of working on my project. Generally speaking
(about 99% of the time), you should do NVT first. Weak temperature
coupling methods like Berendsen or V-rescale are used because the
system is far from equilibrium and any initial clashes will induce
huge temperature fluctuations if you apply the Nose-Hoover method.
The only explanation for these observations lies in the primary
literature for the thermostat algorithms. I'll warn you, the math
is heavy. Sorry to say there is no quick link to provide. I've
never seen anyone be able to give a concise description of these
algorithms, let alone the difference between them :)
I used Parrinello-Rahman for the lysozyme NPT since, during NPT, the
system is less sensitive to pressure oscillations once NVT has been
done. In the umbrella sampling tutorial, since I did not do NVT, I
maintained a weak coupling method. This is because the first
equilibration you do should always use some form of weak coupling.
Certainly during actual data collection you should use Nose-Hoover
or V-rescale for your thermostat and Parrinello-Rahman for your
barostat. The Berendsen method is quick and convenient, but does
not generate a proper statistical mechanical ensemble. Because of
this, the temperature and pressure distributions it generates are
non-physical and the free energy surface of the simulation
trajectory is not correct.
Let us know if you have any further questions.
-Justin
Ravi Kappiyoor wrote:
Sorry to bother you again, but I have some questions regarding
the MD simulation after getting the protein structure. As Joe
had suggested previously, I've used Modeler to create a
structure based on multiple templates (attached). I used 1KAP
and 1GO8 as they had better sequence identities (28 and 26%
respectively, as opposed to 21% and 19% for the other two
templates). I've been going through Justin's lysozyme and
umbrella sampling tutorials (except using the attached resilin
pdb instead of the pdb files that the tutorial files mention).
However, after going through both of them, I have a few
questions. In the lysozyme tutorial, after running an energy
minimization, an NVT minimization was done before an NPT
minimization, while the umbrella tutorial simply went straight
from energy minimization to NPT. I was wondering why NVT was
skipped in the umbrella tutorial. Also, in the coupling,
different coupling parameters were used between the two
simulations (the lysozyme used Parrinello-Rahman whereas the
umbrella used Brendsen coupling). A quick Google search didn't
seem to help me find the differences between the two, so I was
wondering if you had a link that would let me know the
difference between those two schemes. If not, I'll try and
search more thoroughly to see if I can find something. Sorry
once again to ask for so much help, but I've never worked with
MD before, so I'm trying to learn as much as I can before really
running any actual simulations.
--
Thanks,
Ravi Kappiyoor
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
Thanks,
Ravi Kappiyoor
--
========================================
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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