Dear Berk<br><br><div class="gmail_quote">2012/7/16 Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>On 7/16/12 13:05 , francesco oteri
wrote:<br>
</div>
<blockquote type="cite">
<div>
<div>Dear gromacs developers,</div>
<div>I am trying to implement in gromacs 4.5.5 a particular
Hemiltonian Replica Exchange tecnique. </div>
<div>Right now, at every exchange attempt in do_md, I figured
out how to access at the potential </div>
<div>energy of replica A (=configuration A at temperature A) and
B (=configuration B at temperature B) and so on.</div>
<div> </div>
<div>In my case, each replica has the same temperature, but
there is a different Hemiltonian equation for every replica. </div>
<div>The different Hemiltonian are obtained simply changing the
force field parameters in the input topology so I dont </div>
<div>need to modify anything in gromacs.</div>
<div><br>
</div>
<div>But at every exchange attempt I have to test if the
configuration B can exist in the state A so I need to
calculate</div>
<div>its potential energy using the force field data of replica
A. </div>
<div><br>
</div>
<div>I found that function sum_epot calculates the potential
energy but I suspect that it uses values calculated in </div>
<div>do_force since sum_epot is called by do_force_lowlevel in
turn called by do_force. </div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>So my question is, should I call do_force in replica A with
coordinates from replica B reach my goal?</div>
</div>
</blockquote></div></div>
Yes.<br>
Are you changing bonded and/or non-bonded parameters?<br>
Some non-bonded parameters might be preprocessed, so you might need
reprocess those<br>
and them reprocesses again to get back to the original state.<br>
<br></div></blockquote><div><br></div><div>Which parameters need such a preprocessing?</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Note that 4.6 will have proper Hamiltonian replica exchange, but
that will use the lambda coupling<br>
parameter approach. If you need to do something similar, it might be
much simpler to use this code.<br>
<br></div></blockquote><div><br></div><div><br></div><div><div>Actually I did it but I the performance decrease a lot (2x). </div><div>In particular I run the same run with free_energy = yes and free_energy = no and in the second case the run is 2times faster. </div>
<div>I found in the mailing list that this performance drop is known. </div><div><br></div><div>Since I dont need to change lambda along the simulation, I prefer using a modified input topology and running a normal REMD changing something in repl_ex.c and md.c. </div>
<div><br></div><div>Of course, any suggestions to improve performance are wellcome :)</div></div><div><br></div><div><br></div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Cheers,<br>
<br>
Berk<br>
<blockquote type="cite">
<div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>
Francesco</div>
</div>
<div><br>
</div>
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</blockquote>
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</div>
<br>--<br>
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www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>