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<DIV><FONT size=2 face=Arial><SPAN class=296300714-11102011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=296300714-11102011>I have a protein
with 5 different ligands. For each system I made 30ns simulation and I
calculated the lifetime of the H-bonds between protein and ligand with the
command:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=296300714-11102011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=296300714-11102011>g_hbond -f traj.xtc
-s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac hbac.xvg -life
hblife.xvg</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=296300714-11102011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=296300714-11102011>During all
calculations, the printout of the command gave the same
warning:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=296300714-11102011>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><FONT
face="Times New Roman"></FONT> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><FONT
face="Times New Roman">WARNING: Correlation function is probably not long
enough</FONT></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><FONT
face="Times New Roman"></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><FONT
face="Times New Roman">because the standard deviation in the tail of C(t) >
0.001</FONT></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><FONT size=3
face="Times New Roman"></FONT> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><SPAN
class=296300714-11102011>and as a matter of fact, the tail of C(t) <SPAN
style="FONT-FAMILY: 'DejaVu Sans Mono'; FONT-SIZE: 10pt; mso-fareast-font-family: 'DejaVu Sans'; mso-hansi-font-family: 'DejaVu Sans Mono'; mso-bidi-font-family: 'DejaVu Sans'; mso-font-kerning: .5pt; mso-ansi-language: IT; mso-fareast-language: HI; mso-bidi-language: HI"><FONT
face="Times New Roman">(average C(t) over second half of acf)
</FONT></SPAN>reported below this warning was always > 0.001, generally
comprised between 0.45 and 0.74 with two exceptions: a value of 0.02+/-0.03 and
a value of 0.04+/-0.01.</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><SPAN
class=296300714-11102011>Therefore, I'm asking if the forward values considered
as lifetimes are reliable or not, and in case, what can I do to avoid this
warning.</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><SPAN
class=296300714-11102011></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><SPAN
class=296300714-11102011>Thank you very much and best regards</SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=PreformattedText><SPAN
class=296300714-11102011>Anna</SPAN></SPAN></FONT></P></DIV>
<DIV> </DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with a gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV>
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