Re: LES with PME and neutralizing charges

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Mar 09 2006 - 13:03:10 CST

Dear Raffaele,

I dont know exactly how LES is implemented in NAMD, but I have
experience with LES in AMBER. .. and your questions are more general ...
First of all, you need one ion for 1 charged residue, no matter how many
copies you have.

Among other papers, LES in explicit solvent + PME has been documented in
Carlos's Simmerling paper (see ref 1 below) ... For another application
of LES in explicit solvent + PME, you might want to take a look at
references 2 and 3 below.

A pretty good comprenhensible introduction to LES (to read before
reading other papers) you can find in the user manual of AMBER8 software
(page 183 to 193, 269 to 270). Just ignore the practical aspects of
using LES in AMBER .... (http://amber.scripps.edu/doc8/index.html)

As for the question whether there is any reason not to do LES in
explicit solvent, my answer is no, there isnt .. However, the explicit
solvent does not allow the LES copies to drift apart from eachother and
explore different conformations (at least that's the case for nucleic
acids -- and people should correct me on this if that's not the case for
proteins) ... but you would definetely benefit from lowering the energy
barriers of conformational transitions (but be carefull with an
excessive lowering ... as discussed in ref. 2 and 3 below) ....

Best
vlad

1. Simmerling, C., Miller, J.L., and Kollman, P.A. 1998b. Combined locally
enhanced sampling and particle mesh Ewald as a strategy to
locate the experimental structure of a nonhelical nucleic acid. J.
Am. Chem. Soc. 120: 71497155.

2. Cojocaru et al., RNA 2005, 11, 197-209
3. Cojocaru et al., Nucleic Acids Research 2005, 33, 3435-3446

curcio wrote:

>Hi all,
>
>I have a question concerning the usage of locally enhanced sampling (LES ) as
>provided by NAMD:
>
>Is there any reason why not using LES together with the PME-method?
>
>If no, i.e. it is fine to combine LES with PME, then how should "replicated"
>charges (i.e. multiple copies of a charged part, e.g. of the sidechain of a
>lysine) be taken into account when neutralizing the charge with counterions?
>Imagine there are five copies of the sidechain of a lysine instead of only one
>- how many negatively charged ions should be used to account for the charge
>of this replicated lysine? Five negatively charged ions or is one already
>sufficient for instance because the electrostatic interaction is also divided
>by five?
>
>Thanks for your help,
>
>Raffaele
>
>
>

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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