AMBER Archive (2009)

Subject: RE: [AMBER] What is the purpose to do the bond constraints?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun May 17 2009 - 22:38:52 CDT

Hi Lin,

I am not entirely sure I understand your question here. If you are referring
to why hydrogens are constrained by shake. This is to allow the use of
longer timesteps since it removes the highest frequency oscillations in the
system. I would suggest doing a literature search on 'SHAKE' or following
the references to it in the AMBER manual.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Chih-Ying Lin
> Sent: Sunday, May 17, 2009 3:09 PM
> To: AMBER Mailing List
> Subject: [AMBER] What is the purpose to do the bond constraints?
>
>
>
> Hi
>
> The atoms are connected by covalent bonds and the atoms are restricted
> by the overall force field.
> What is the purpose to do the bond constraints?
> What do the "bond constraints" mean?
>
> Thank you
> Lin
>
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