<br><font size=2 face="sans-serif">Dear all,</font>
<br>
<br><font size=2 face="sans-serif">I would like to write down here some
remarks about my Replica Exchange Molecular Dynamics simulation that finally
thanks to all the advices has been successfully (partially performed).</font>
<br>
<br><font size=2 face="sans-serif">1. The real problem of my simulation
(described in the following post: http://www.gromacs.org/pipermail/gmx-users/2005-October/017715.html
) was inded the temperature distribution and the difference of temperature
I had between replicas. therefore, I have changed completely my mind and
used this T setup:</font>
<br>
<br><font size=2 face="Courier New">280.0 281.0 282.1 283.2 284.3 285.6
286.8 288.2 289.6 291.0 292.5 294.1 295.7 297.3 299.1 300.8 302.7 304.6
306.5 308.5 310.6 312.7 314.8 317.1 319.3 321.7 324.1 326.5 329.0 331.6
334.2 336.8 339.6 342.3 345.2 348.1 351.0 354.0 357.1 360.2 363.3 366.6
369.8 373.2 376.6 380.0</font>
<br>
<br><font size=2 face="sans-serif">reducing the global time interval and
also the difference of temperature between the single replicas according
to Berk Hess advice.</font>
<br><font size=2 face="sans-serif">Now the REMD is really ... exchanging
replicas ! And everything sems to be fine and it works really well. Many
thanx to all who gave me advices.</font>
<br>
<br><font size=2 face="sans-serif">2. A question/ suggestion: REMD implementation
is only set up for single CPU .... but what about giving the possibility
of distributing a replica on many CPUs instead of using one processor only
? Is it a choice or are there any problems of implementationof such a feature
??</font>
<br>
<br><font size=2 face="sans-serif">Bye</font>
<br>
<br><font size=2 face="sans-serif">LM</font>
<br>
<br>
<br><font size=2 face="sans-serif"> </font>
<br><font size=2 face="sans-serif">-----------------------------------------------------------------------------<br>
<br>
Luca Mollica<br>
ZRL-IBM Research Center<br>
Saumerstrasse 4<br>
8803, Rueschlikon (Zurich)<br>
CH<br>
<br>
Tel: 0041 - 447248217<br>
<br>
email: YLU@zurich.ibm.com <br>
email(alt): ZRLYLU@ch.ibm.com <br>
</font>