AMBER Archive (2009)

Subject: Re: [AMBER] Regarding rigid bond

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 01 2009 - 06:55:17 CST

thanks Dave for correcting me, I didn't know about that option...

On Tue, Dec 1, 2009 at 7:50 AM, case <case_at_biomaps.rutgers.edu> wrote:

> On Tue, Dec 01, 2009, Carlos Simmerling wrote:
>
> > the only option is to constrain all bonds. you cannot do this for some
> bonds
> > and not for others unless you modify the code (which is not possible
> unless
> > you have programming experience).
>
> There is the "noshakemask" option that might help: you would turn on SHAKE,
> then turn it off for the parts where you don't want it. Check carefully
> that
> you are getting what you really want.
>
> ....dac
>
>
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