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<DIV><FONT face=Arial size=2>Hi gromacs users / developers</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I'm trying to estimate a free energy from MD
of the</FONT></DIV>
<DIV><FONT face=Arial size=2>complex of large protein (> 1000 AA) and
small ligand</FONT></DIV>
<DIV><FONT face=Arial size=2>in order to compare free energies of two binding
modes</FONT></DIV>
<DIV><FONT face=Arial size=2>which are different in conformation but same in
topology.</FONT></DIV>
<DIV><FONT face=Arial size=2>This system is huge (> 80 000 atoms)
and the </FONT><FONT face=Arial size=2>potential</FONT></DIV>
<DIV><FONT face=Arial size=2>energy in absolute <FONT face=Arial
size=2>magnitude is high (- 10^6 kJmol-1).</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2>When trying g_energy i recieve "inf" instead
of free</FONT></DIV>
<DIV><FONT face=Arial size=2>energy estimate. I would like to ask wether this is
due</FONT></DIV>
<DIV><FONT face=Arial size=2>to the fact that E/kT is too low so e^(E/kT)
is close to</FONT></DIV>
<DIV><FONT face=Arial size=2>zero (out of precision of calculation) ? Than it
would be</FONT></DIV>
<DIV><FONT face=Arial size=2>possible to calculate it from the </FONT><FONT
face=Arial size=2>output file. Is it correct</FONT></DIV>
<DIV><FONT face=Arial size=2>to set potential energy (# 9 in g_energy menu) for
such</FONT></DIV>
<DIV><FONT face=Arial size=2>free-</FONT><FONT face=Arial size=2>energy
estimation ?</FONT></DIV>
<DIV><FONT face=Arial size=2>Thank you very much for previous
answers.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Vojtech Spiwok</FONT></DIV>
<DIV><FONT face=Arial size=2>ICT Prague</FONT></DIV>
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