From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Mon Jul 01 2013 - 14:29:56 CDT
I could not agree more with Axel. First, the old Barker and Watts reaction
field algorithm is clearly outdated. What you may have in mind is the 1994
Barker (or the 1995 Tironi et al.) generalized form, which is a
equation. Still, for saline solutions, you will always be better off
even though, as Axel hinted, this is not a panacea. Second, if some MD
codes have kept, probably for historical reasons, old algorithms, which
have been surpassed ever since, it does not mean that these algorithms
should be ported to NAMD. Third, the burden is definitely on you to show
that whatever reaction field variant you have in mind, it would be worth
implementing it. Word of wisdom -- pick your favorite MD code featuring
either the old Barker and Watts reaction field method or its generalized
version, compute the permittivity of water from the r-dependent Kirkwood
factor, and compare the accuracy/cost with PME.
On 7/1/13 7:25 AM, Axel Kohlmeyer wrote:
> On Mon, Jul 1, 2013 at 7:01 AM, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
>> Hi Axel (and other NAMD users),
>> Have you any concrete data showing that simply ignoring the reaction field
>> term makes no difference, at least for homogeneous systems?
> have you looked at a paper describing the reaction field method and
> studied how it works?
> also, if you want somebody else to implement something, the burden of
> proving that it would be worth it, is on you. not the other way
>> On Sat, Jun 29, 2013 at 6:51 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>> On Fri, Jun 28, 2013 at 8:24 AM, Neelanjana Sengupta
>>> <senguptan_at_gmail.com> wrote:
>>>> Dear NAMD experts,
>>>> Does the NAMD simulation package allow for the Reaction field treatment
>>>> in a
>>>> solvent simulation? I could not find adequate documentation for this. If
>>>> not, are we to expect this soon (as some comparable simulation packages
>>>> already provide this)?
>>> what do you mean by "already"? it is more that particle mesh ewald came
>>>> Some pointers would be highly appreciated.
>>> if you don't want PME, you can turn it off. the result is for all
>>> practical purposes the same, i.e. equally bad for almost anything.
>>>> Thanks and regards,
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Phone: (217) 244-5711 Urbana, Illinois 61801 Fax: (217) 244-6078 E-mail: chipot_at_ks.uiuc.edu Christophe.Chipot_at_edam.uhp-nancy.fr Web: http://www.ks.uiuc.edu/~chipot http://www.edam.uhp-nancy.fr It is hard for France to maintain a thirty-five-hour workweek when China and India have invented a thirty-five-hour workday. Thomas L. Friedman _______________________________________________________________________
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:25 CST