Hi Vlad,
How did you decide that the trajectories could not be reweighted?
Στις 28 Απρ 2014 12:53 ΠΜ, ο χρήστης "Vlad Cojocaru" <
vlad.cojocaru.mpi-muenster.mpg.de> έγραψε:
> Hi Jef, Hi Sourav,
>
> Maybe I can comment further here ...
>
> We did quite a bunch of aMD (only dihedral boost) runs on
> protein/nucleic acid complexes (not published yet) and I can confirm
> that it works well at least qualitatively. Using parameters calculated
> based on the suggestions on the amber manual (3.5 kcal/mol/residue to
> estimate alpha and Ed) did not affect DNA much. However, adding 2 alphas
> to the boost did destroy the DNA at the ends on some of our systems.
>
> However, the problem came when we tried to reweight. We realized that
> the boost was far too high for reweighting even using the second order
> cumulant expansion.
> We came across this paper that I mentioned in my previous email ...
> http://www.ncbi.nlm.nih.gov/pubmed/23781107 and we switched to apply the
> lambda-based scheme for estimating the parameters. The paper suggests
> lambda=0.3 for the protein/membrane system they investigated. However,
> we found 0.3 to be too large or our systems as the reweigthing was still
> compromised. We now switched to test different lamdas and a value of
> 0.15 appears to give very nice trajectories that sample significantly
> more the dynamics of the systems compared with standard MD and can also
> be reweighted. However, we also noticed that in order to get smooth
> profiles upon reweighting we need to run quite long simulations (150 ns
> is by far not enough as the reweighted profiles are still noisy).
>
> This is to share our experience with the particular systems we work
> with. Whether this is applicable to other system, I don't know.
> So,please test for any different system. But I would definitely
> recommend the lambda-based scheme to estimate the parameters (its only 1
> variable to be changed, and therefore easier to run tests with)...
>
> I hope this helps
> Vlad
>
> On 04/27/2014 09:16 PM, Jeff Wereszczynski wrote:
> > Hi Sourav,
> >
> > I haven't looked at the suggestions in the Amber user guide, but I have a
> > pretty good guess as to what they are. It sounds like you are doing a
> > "dual-boost" setup. So here's what I would say.
> >
> > 1. Yes. The number of atoms is typically used for the term that boost
> the
> > complete potential, which is dominated by non bonded terms. Since waters
> > are included in that, you need to include the water atoms.
> >
> > 2. As far as I know, no one has published aMD simulations with nucleic
> > acids. I've played with it a bit, and it works fine. You should include
> > the DNA in the residue count since they are being accelerated by the
> > dihedral term (since they have dihedrals in them). Just keep in mind
> that
> > the suggested aMD parameters were derived mainly for proteins with the
> > amber force field, so you may need to fiddle with the acceleration
> > parameters you use. But the suggestions in the amber user guide should
> get
> > you in the right ballpark.
> >
> > Typically what you want to do is try a number of short simulations with
> > different parameters, using the parameters in the amber user guide as a
> > suggestion, then seeing how it affects your system. If you need more
> > acceleration, try adding a value of alpha (or alphaD) to your thresholds.
> > If you have too much acceleration and you are getting unphysical
> effects,
> > decrease your thresholds by alpha. Other people have different
> > parameterization methods, but in the past this has worked well for me.
> >
> > Cheers,
> >
> > Jeff Wereszczynski
> > Assistant Professor of Physics
> > Illinois Institute of Technology
> > http://www.iit.edu/~jwereszc
> >
> >
> >
> >> Message: 2
> >> Date: Sun, 27 Apr 2014 16:31:08 +0530
> >> From: Sourav Purohit <sour000.gmail.com>
> >> Subject: [AMBER] Accelerated MD
> >> To: AMBER Mailing List <amber.ambermd.org>, Jason Swails
> >> <jason.swails.gmail.com>, ross.rosswalker.co.uk
> >> Message-ID:
> >> <CAFMrzpzPjf1ZN2-V71v=fkeZrDeGNytZsAQSpL7ZxM1xysvs=
> >> w.mail.gmail.com>
> >> Content-Type: text/plain; charset=ISO-8859-1
> >>
> >> Hi all,
> >>
> >> I had some doubts on the method of calculating parameters for
> accelerated
> >> MD as described in the AMBER12 manual (page no.160).
> >>
> >> 1.Does the total number of atoms (taken as 16950 in the example) include
> >> atoms belonging to water molecules also??
> >>
> >> 2.for the calculation of alphaD, only the number of protein residues
> goes
> >> as an input. What if a system has other components like DNA?? Should I
> >> include the DNA residues also??
> >>
> >> Kindly help.
> >>
> >> Thanks.
> >>
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 27 2014 - 16:30:03 PDT
