Re: LES : size

From: Vlad Cojocaru (
Date: Mon Nov 13 2006 - 03:51:46 CST

Dear Arturas,

I have done some LES simulations looking at large conformational changes
in an RNA motif and I had many different system setups including one in
which a whole peace of RNA (17 too 22 bp) was included in a single LES
region. The computational time was not dramatically increased...But I
have done the simulations with AMBER, so I have no idea about how NAMD
behaves (if you want to exact numbers of CPU times from my simulations I
can look them up this week sometime ... they are archived).

However what I believe and I hope its in the interest of people doing
LES simulations is a discussion in my papers about the choice of LES
regions and no. of copies ...Below are the 2 refs.

But of course, its important first that you read first the intial
literature about LES, how it works, advantages and disadvantages

If you have any further questions, I would be pleased to answer you.

Best wishes
* *

Cojocaru V, Nottrott S, Klement R, Jovin TM.
The snRNP 15.5K protein folds its cognate K-turn RNA: a combined
theoretical and biochemical study.RNA. 2005 Feb;11(2):197-209.

* *Cojocaru V, Klement R, Jovin TM.
Loss of G-A base pairs is insufficient for achieving a large opening of
U4 snRNA K-turn motif.
Nucleic Acids Res. 2005 Jun 13;33(10):3435-46. Print 2005.

Arturas Ziemys wrote:

>1) In the manual of NAMD there is now clue about how many atoms can be included into LES. Is there any limitations and considerations about it ?
>2) How calculation time depends on number of atoms and number of copies ?
>3) Is it effective for crossing enthalpic barriers, or entropy barriers, or both ?

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

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