Hi guys,
Jason made a good point in another thread about ff14ipq. The _true_ torsion
potentials are actually the sum of the dihedral energy plus the 1-4 vdW and
1-4 electrostatic energies as well. I wonder how you calculate the "average
dihedral energy" from AMBER output to decide the aMD dihedral boost value.
Do you count only the "DIHED" values or the "1-4 NB" and "1-4 EEL" too?
thanks,
Thomas
On 28 April 2014 08:15, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>wrote:
> Hi Thomas,
>
> Well, the reweighted profiles for different structural properties were
> very noisy and therefore useless.
> See Daniel's answer as well.
>
> Vlad
>
> Sent from my android device.
>
> -----Original Message-----
> From: Thomas Evangelidis <tevang3.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Mon, 28 Apr 2014 1:30 AM
> Subject: Re: [AMBER] Accelerated MD
>
> 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
> >
> _______________________________________________
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--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Apr 28 2014 - 15:00:08 PDT
