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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:<br>
<br>
1) to use its replica exchange algorithm to code something for gmx;<br>
<br>
2) to try and implement the GROMOS/GROMACS ff in MMTSB.<br>
<br>
Martina<br>
<br>
Ilya Chorny wrote:<br>
<blockquote type="cite" cite="mid:1069450020.24167.0.camel@chaos.compbio.ucsf.edu">
<pre wrap="">Is it set up to work with gromacs? Looks like just CHARMM and Amber.<br><br>Ilya<br><br>On Fri, 2003-11-21 at 12:29, Martina Bertsch, PhD wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">Greetings, Ilya.<br><br>Replica exchange has been implemented in the Multiscale Modeling Tools <br>for Structural Biology (MMTSB), a joint effort of the Scripps Research <br>Institute, Pittsburgh Supercomputing Center and several universities. <br>The toolkit can be downloaded, along with extensive documentation from:<br><br><a class="moz-txt-link-freetext" href="http://mmtsb.scripps.edu/software/mmtsbtoolset.html">http://mmtsb.scripps.edu/software/mmtsbtoolset.html</a><br><br>Particularly interesting for you might be the PSC 2003 Workshop lecture <br>notes and tutorial #6 on replica exchange.<br><br>Regards,<br><br>Martina Bertsch, Ph.D.<br>Northwestern University<br>Feinberg School of Medicine<br>Molecular Pharmacology and Biological Chemistry<br>303 East Chicago Avenue<br>Chicago, IL 60611<br><br><br>Ilya Chorny wrote:<br><br></pre>
<blockquote type="cite">
<pre wrap="">Has anyone done replica exchange in gromacs. (i.e written the scripts to<br>due replica exchange). It seems like it would be pretty straight forward<br>but I don't want to reinvent the wheel if its already been invented.<br><br>Thanks<br><br>Ilya<br><br></pre>
</blockquote>
<pre wrap=""><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></pre>
</blockquote>
<pre wrap=""><!----><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><br><br></pre>
</blockquote>
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