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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi STEVE </SPAN><SPAN lang=EN-US
style="FONT-SIZE: 10pt; FONT-FAMILY: Wingdings; mso-ascii-font-family: Arial; mso-hansi-font-family: Arial; mso-bidi-font-family: Arial; mso-char-type: symbol; mso-symbol-font-family: Wingdings"><SPAN
style="mso-char-type: symbol; mso-symbol-font-family: Wingdings">J</SPAN></SPAN><SPAN
lang=EN-US><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I found it in mdrun.log. Look
for "ewald correction". <o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Do you know how to evaluate this LR
coulomb <o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">interaction energy between protein
and ligand?</SPAN><SPAN lang=EN-US><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>David wrote that I missed some terms
</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">but I don’t know which ones!.<SPAN
style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>My evaluated energy <SPAN
style="mso-spacerun: yes"> </SPAN>seems wrong.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Please let me know if you find a right way to
</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>do it.</FONT></SPAN></P><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: PL; mso-bidi-language: AR-SA">Michal <SPAN
style="mso-spacerun: yes"> </SPAN></SPAN></FONT></DIV>
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<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>Hi Michal,<BR><BR>It sounds like we are doing similar things.<BR><BR>Can
you explain to me how you were able to use mdrun -rerun -debug to get<BR>the
correction terms? I tried running this yesterday, and it generated<BR>some
files (ctab.xvg, dtab.xvg, rtab.xvg, mdrun.log), but I have no idea<BR>where to
look for the correction.<BR><BR>Thanks!<BR>Steve<BR><BR><BR>On Wed, 4 May 2005,
Michal Kolinski wrote:<BR><BR>> I tried to evaluate LR Coulomb interaction
energy for ligand and protein. My system contains<BR>> membrane,
ligand, TM protein and ions. I did three reruns of my trajectory:<BR>>
1) leaving charges on ligand, zeroing rest<BR>> 2) leaving charges on
protein, zeroing rest<BR>> 3) leaving charges on protein and ligand, zeroing
rest.<BR>> Then I calculated LR Coulomb interaction energy for prot-lig
(Elr_c(ligand-protein)):<BR>><BR>><BR>> Elr_c(protein-ligand) =
Elr_c(ligand-ligand) + Elr_c(ligand-protein)
+<BR>>
Elr_c(protein-protein)<BR>> in my
case:<BR>><BR>> 3 = 1 + Elr_c(ligand-protein) +
2<BR>><BR>> I also included long range corrections for each of the
reruns that I found using -rerun -debug option.<BR>> Is this a right way to
estimate LR coulomb interaction energy between two molecules, my estimated
energy seems wrong 13.567.<BR>> Please give me some comment on
this.<BR>> Thank you in
advance.<BR>><BR>><BR><BR><BR></DIV></BODY></HTML>