From: Jeff Wereszczynski (jwereszc_at_iit.edu)
Date: Thu Nov 07 2013 - 10:46:59 CST
Something else to keep in mind is that most of the back of the envelope
estimates for initial aMD parameters that have been quoted in this thread
are based upon the amber force field. The charmm force field (which was
used in this study) has different dihedral energies, so that could
contribute to different boosting parameters.
Also, I don't see any reason from a theoretical standpoint why you couldn't
use aMD with an external electric field. I don't know of anyone that's
done that, but it should be straightforward. Your potential will be
position dependent, but I would think the overall electrostatic energy of
the system would dominate your potential function anyway, so there
shouldn't be too much worry about needing position-dependent boost terms
(which is good, because that would be difficult to do from a computational
standpoint). The only question is if the code is set up to properly at
your energy from the electric field into the boost. My guess is yes, but
thats just a guess. I'd say give it a shot and compare the aMD outputs for
applied boosts to what you would expect from the aMD equations and make
sure they match.
Cheers,
Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology
http://www.iit.edu/~jwereszc
On Thu, Nov 7, 2013 at 9:59 AM, Thomas Evangelidis <tevang3_at_gmail.com>wrote:
>
>
>
>> 3. You might also find this paper interesting:
>> http://www.pnas.org/content/110/27/10982.full
>> There is some discussion in the SI about choosing aMD parameters for a
>> dual-boost setup for a different GPCR that may be helpful.
>>
>> Very good one! The first one I see to implement dual-boost aMD on the
> whole protein-membrane system. The authors introduce a different empirical
> rule to choose dihedral Energy cutoff and alpha value, but use the old rule
> for the total Potential Energy threshold and the respective alpha:
>
> Edihed = Vdihed_avg + lamda*Vdihed_avg
> ádihed= lamda*Vdihed_avg/5
> Etotal = Vtotal_avg + 0.2*Natoms
> á total = 0.2*Natoms
>
>
> Jeff, since you are very familiar with the physics behind aMD and its
> effects on system dynamics, I wonder if you could comment on my recent post
> about combination of aMD with an external electric field:
>
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/1718.html
>
> thanks,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang_at_pharm.uoa.gr
>
> tevang3_at_gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
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