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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
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<p class=MsoNormal><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> <span class=GramE>Alexey
Romanov [mailto:Alexey.Romanov@algodign.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b></span> Wednesday, December
04, 2002 1:12 PM<br>
<b><span style='font-weight:bold'>To:</span></b> 'gmx-users@gromacs.org'<br>
<b><span style='font-weight:bold'>Subject:</span></b> about atom perturbation
in TI</span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-US'>Hi, GMX users!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-US'>Currently I am working with
thermodynamic integration options <font color=navy><span style='color:navy'>(slow
growth) </span></font>of <span class=SpellE>gromacs</span> (for example -
perturbing charges of molecule to nothing in water solvent).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-US'>All works fine, but when I
try to do this for molecule in vacuum (without solvation), I always get zero
free energy change. I think, that it’s not correct, because the charges
in perturbed molecule have an effect on other charges of the same molecule, in
other words, free energy of molecule charging in vacuum must be nonzero. Is it a
bug, or<span style='mso-spacerun:yes'> </span>may be, in Gromacs molecule
perturbations are seen only to the other molecules?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-US'>Regards<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-US'>Alex Romanov,<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:City><st1:place><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial;mso-ansi-language:EN-US'>Moscow</span></font></st1:place></st1:City><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial;
mso-ansi-language:EN-US'>.<span style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
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