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<div class="moz-cite-prefix">On 7/16/12 13:05 , francesco oteri
wrote:<br>
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<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>
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>
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>
Cheers,<br>
<br>
Berk<br>
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<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>
Francesco</div>
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