AMBER Archive (2004)

Subject: Re: AMBER: LES methodology question

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Feb 20 2004 - 07:01:06 CST

This is discussed in the 12 pages on LES in the AMBER7 manual.
as well as in the literature.

to summarize, you only get multiple conformations sampled
at 1 time for the region that you copy. If you want to simultaneously
sample multiple helix-loop-helix conformations, then
you need to copy that. if you want to sample only multiple
loop conformations, copy that. It depends on how coupled
your helices and loop are. longer regions give more independence
to the copies, but more regions gives improved copy-copy
averaging that smooths the energy surface. It's a compromise
and there is not always an obvious answer without doing some
tests.

long regions can also require more memory when using PME,
so it may be good to start with helix, loop and helix all in
their own regions.
carlos

----- Original Message -----
From: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
To: "amber list" <amber_at_scripps.edu>
Sent: Friday, February 20, 2004 7:12 AM
Subject: AMBER: LES methodology question

> Dear Amber users,
> Iam simulating an RNA molecule using LES. My RNA has three
> interesting subregions (2 helices and 1 loop) connected to eachother in
> the order helix-loop-helix. I want to make LES subspace for all these
> regions using 5 copies. Now ..there are 2 posibilities (or probably more):
> 1. Make 1 LES subspace and replace the entire region (~15 nucleotides)
> with 5 copies of it
> 2. Make 1 LES subspace for the first helix (5 copies), another one (5
> copies) for the loop and another one for the second helix (5 copies).
>
> I would appreciate if somebody could comment on advantages and
> disadvantages of each of these posibilies. More in general I would like
> to have a discussion about 1 LES subspace of the region of interest
> (more atoms copied) versus spliting the region of interest into more
> than 1 LES subspace (more LES regions but les atoms copied per region)
> Thank you very much
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
>
>
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