AMBER Archive (2009)

Subject: Re: [AMBER] -MMTSB instalation flag ?

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue Feb 03 2009 - 11:38:11 CST


Hi,

Yes, to clarify as far as I know,
(I haven't looked at MMTSB for several years)
only the replica exchange feature of MMTSB cannot be used
with Amber (unless you try building sander with -mmtsb).
Conversely, everything else probably works fine and only
requires a normal Amber installation.

Scott

On Tue, 3 Feb 2009, Marek MalĂ½ wrote:

> As you wrote, flag (-mmtsb) is already present in version Amber 10.
>
> If I understood well this instalation flag is not so crucial for later
> usage of MMTSB tools with Amber support and that is the main information
> for me.
>
>
> Dne Tue, 03 Feb 2009 18:06:47 +0100 Scott Brozell <sbrozell_at_scripps.edu>
> napsal/-a:
>
> >On Tue, 3 Feb 2009, Marek MalĂ½ wrote:
> >
> > >what is the exact meaning of this Amber instalation flag:
> > >
> > >"-mmtsb Request building sander for MMTSB" ?
> > >
> > >It allows some significant improvement of "collaboration" of Amber and
> > >MMTSB
> > >tools ?
> > >
> > >What are the prerequisities to use this flag. For example is the MMTSB
> > >tools
> > >required to be installed
> > >before instlallation of AMBER with -mmtsb flag ?
> > >
> > >In MMTSB instal page I just found, that if some MMTSB user want to benefit
> > >from the possibility
> > >to use MMTSB in combination with Amber, he just should set AMBERHOME
> > >variable,
> > >which every
> > >Amber user has set anyway. I didn't find any notice that if I want to use
> > >MMTSB in combination with Amber,
> > >compilation of Amber with -mmtsb is required.
> >
> >This is an old implementation of replica exchange.
> >In Amber8, the MMTSB Toolkit was used as a "driver" program,
> >which spawned off independent sander jobs,
> >and took care of collecting the results and making the replica exchanges.
> >See p 149 of the Amber8 manual.
> >
> >This feature was only used a little as far as I know.
> >However, it appears to still exist in Amber9 and Amber10 although it's
> >undocumented. If you have an mmtsb server then you might be able to
> >get it to work, but you are strongly encouraged to use the documented
> >replica exchange method.
> >
> >As far as the MMTSB Amber documentation, Dave Case should probably
> >update that.
> >

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