AMBER Archive (2009)
Subject: Re: [AMBER] -MMTSB instalation flag ?
From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue Feb 03 2009 - 11:06:47 CST
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
AMBER mailing list