[gmx-users] Re: Resilin Project
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 5 01:26:23 CEST 2010
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
========================================
More information about the gromacs.org_gmx-users
mailing list