[gmx-users] replica exchange

[Martina Bertsch, PhD]

As far as I know, only the AMBER AND CHARMM ff's are implemented in 
MMTSB. However, being open source, MMTSB offers you two possibilities:

1) to use its replica exchange algorithm to code something for gmx;

2) to try and implement the GROMOS/GROMACS ff in MMTSB.

Martina

Ilya Chorny wrote:

>Is it set up to work with gromacs? Looks like just CHARMM and Amber.
>
>Ilya
>
>On Fri, 2003-11-21 at 12:29, Martina Bertsch, PhD wrote:
>
>>Greetings, Ilya.
>>
>>Replica exchange has been implemented in the Multiscale Modeling Tools 
>>for Structural Biology (MMTSB), a joint effort of the Scripps Research 
>>Institute, Pittsburgh Supercomputing Center and several universities. 
>>The toolkit can be downloaded, along with extensive documentation from:
>>
>>http://mmtsb.scripps.edu/software/mmtsbtoolset.html
>>
>>Particularly interesting for you might be the PSC 2003 Workshop lecture 
>>notes and tutorial #6 on replica exchange.
>>
>>Regards,
>>
>>Martina Bertsch, Ph.D.
>>Northwestern University
>>Feinberg School of Medicine
>>Molecular Pharmacology and Biological Chemistry
>>303 East Chicago Avenue
>>Chicago, IL 60611
>>
>>
>>Ilya Chorny wrote:
>>
>>>Has anyone done replica exchange in gromacs. (i.e written the scripts to
>>>due replica exchange). It seems like it would be pretty straight forward
>>>but I don't want to reinvent the wheel if its already been invented.
>>>
>>>Thanks
>>>
>>>Ilya
>>>
>>
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>
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