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<PRE>Hello,</PRE>
I am trying to do REMD for a protein unfolding. I am following the information given in <A href="http://wiki.gromacs.org/index.php/REMD">http://wiki.gromacs.org/index.php/REMD</A> but I am completely new in these type of simulations. I would like to ask two questions to more advanced users. I hope you could help me:<BR>
<BR>
-I have seen that the<RTE_TEXT></RTE_TEXT> exchange rate should be typically between 0.2 and 0.3. Where can I extract the exchange rate from my outputs? For example in the output below the exchange rate would be "Repl pr .08 .00 .13"? Should I calculate a mean for all exchanges and all replicas and check if this mean is between 0.2 and 0.3?<BR><BR>Repl 0 <-> 1 dE = 2.492e+00<BR>Repl ex 0 1 2 3 4 5<BR>Repl pr .08 .00 .13<BR>Replica exchange at step 2000 time 4<BR>Repl ex 0 1 2 3 x 4 5<BR>Repl pr .00 1.0<BR>
<BR>
-Another question is about restarting simulations. I have though doing it with tpbconv and then concatenate the .log files to use demux.pl. Is this correct?<BR>
<BR>
Thank you very much for your help.<BR>
Best wishes, <BR>
<BR>
Rebeca Garcia<BR>
Parc Cientific of Barcelona<BR>
Barcelona University<BR>
<A href="mailto:regafan@hotmail.com">regafan@hotmail.com</A><BR><BR><br /><hr />Comparte tus fotos con tus amigos. Más fácil con <a href='http://download.live.com' target='_new'>Windows Live</a></body>
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