AMBER Archive (2009)

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

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Tue Feb 03 2009 - 11:15:04 CST

Dear Scott,

thanks a lot for a prompt answer.

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.

   Thanks again !

      Marek

Dne Tue, 03 Feb 2009 18:06:47 +0100 Scott Brozell <sbrozell_at_scripps.edu>
napsal/-a:

> Hi,
>
> On Tue, 3 Feb 2009, Marek Malý 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.
>
> Scott
>
>
>
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