AMBER Archive (2008)

Subject: Re: AMBER: Eigenmode dynamics - imaging traj

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Jun 18 2008 - 08:33:07 CDT


If you talk about iRED.....

Since iRED use N-H vector, you don't have to image.
If you want, you can translate.
However DON'T ROTATE. DON'T DO rms fitting like the manual says (fitting is
required for other analysis)

*J Mol Biol*<http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WK7-4PSC2F3-3-1&_cdi=6899&_user=2268449&_orig=search&_coverDate=12%2F07%2F2007&_sk=996259995&view=c&wchp=dGLzVlz-zSkzk&md5=03aa63e5d8f632c80e2168663ce257b9&ie=/sdarticle.pdf>374:977-992.
J. Am. Chem. Soc. 124, 45224534

On Wed, Jun 18, 2008 at 7:16 AM, E.M. <pckboy_at_gmail.com> wrote:

> What is IREP?. What are you talking about? paper?
>
> Edu
> fatima.chami_at_durham.ac.uk wrote:
>
>> Hi folks,
>>
>> do I have to image the md trajectories before aligning them to reference
>> frame when computing the time correlation with IREP approach
>>
>> any help on this...
>>
>> fatima
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-- 
Best wishes,

Myunggi Yi PhD ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi

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