for another system (at 250K) also i have calculated hydrogen bond lifetime using:<div>hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250</div><div> whose output is :</div><div><div><div>acf 14477/14477</div>
<div>normalization for c(t)=0.0135742 for gh(t)=6.78702e-05 <br>hydogen bond thermodynamics at T=250K</div><div>fitting parameters chi^2 = 3.89447e-06</div><div>Type rate time DG chi^2</div><div>
forward -1.201 -0.833 -666.000 3.89447e-06</div><div>backward -0.354 -2.823 -666.000 </div><div>......</div><div><br></div><div>Here again i am getting negative hydrogen bond lifetime.</div><div>Please suggest me where i am getting wrong and what does negative lifetime mean?</div>
<div>Thank you in advance.</div><div><br></div><div><br><div class="gmail_quote">On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><br><div><div>29 mar 2012 kl. 18.47 skrev Nidhi Katyal:</div><div><div class="h5"><br>
<blockquote type="cite">Dear All<div>I would like to know the strength of the given bond by calculating the lifetime of that bond.For the same reason i used:</div><div>g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg</div>
<div>
and i got:</div><div>Type Rate(1/ps) Time(ps) ...</div><div>Forward -0.182 -5.495</div><div>.......</div><div>HB lifetime=50.60ps</div><div>Note that the lifetime obtained in this manner is close to useless.Use the -ac option instead and check the forward lifetime.</div>
<div>..</div><div>Will it be correct to say that lifetime is -5.495ps (looking at forward time)? But then what does negative lifetime implies?</div><div>Thanks in advance.</div></blockquote><div><br></div></div></div><div>
Seems weird. Could the amount of underlying data be insufficient? Have you looked at the acf?</div><div><br></div><div>Erik</div><br><blockquote type="cite">
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<div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div>
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