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On 5/12/2011 12:17 AM, Vasileios Tatsis wrote:
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cite="mid:1323004629.51878.YahooMailNeo@web26706.mail.ukl.yahoo.com"
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<div>Greetings GrOmAcS Users,</div>
<div><br>
</div>
<div>I want to calculate the free energy, for different
(de)protonation states, of a certain compound.</div>
<div>This requires to edit by hand many topology files.</div>
<div><br>
</div>
<div>Is there a code that can do it on-the-fly or any
ideas(algorithm) how it can be done automatically?</div>
<br>
</div>
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<br>
Since you'd need to add/remove the proton and perhaps change the
atom type to which it was bound and maybe its other proton atom
types, it is hard to come up with a general algorithm that is worth
the time to implement.<br>
<br>
Mark<br>
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