<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<br><div><blockquote type="cite"><div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div dir="ltr"><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b><span class="Apple-style-span" style="font-weight: normal; -webkit-text-stroke-width: 0;"><br></span>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Laercio Pol Fachin <<a href="mailto:laercio_pf@yahoo.com.br">laercio_pf@yahoo.com.br</a>></font></span></div></blockquote></div></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 34px; text-indent: -34px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">September 30, 2008 9:50:48 AM EDT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 21px; text-indent: -21px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 50px; text-indent: -50px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>[gmx-users] Hydrogen Bond Lifetime</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 58px; text-indent: -58px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Reply-To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:laercio_pf@yahoo.com.br">laercio_pf@yahoo.com.br</a>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td valign="top" style="font: inherit;">Hi, all.<br><br>I am analyzing the hydrogen bond lifetime of water molecules around polar atoms of my molecule. However, I have faced different HB lifetime definitions in different sources. A sample of what I obtained employing g_hbond is below:<br><br>"g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 10000"<br><br>Type Rate (1/ps) Time (ps) DG (kJ/mol)<br>Forward 0.797 1.254 5.089<br>Backward 0.061 16.475 11.474<br>One-way 1.323 0.756 3.835<br>Integral 0.948 1.055 4.661<br>Relaxation 2.195 0.456 2.579<br><br># In GROMACS 3.3 manual, page 171, it is said that "the integral of C(t) gives a rough estimate of the average H-bond lifetime", which points to a HB lifetime of 1.055 ps (right?);<br># On the other hand, in previous discussion in this list, I have found that "according to Luzar the time corresponding to the forward rate constant should be regarded as 'the' hbond lifetime", which points to a HB lifetime of 0.797;<br><br>Can anyone please clarify such points?<br><br></td></tr></tbody></table></blockquote><div><br></div><div>Hi,</div><div><br></div><div>The HB definitions and associated lifetimes are a bit arbitrary, so there' s always going to be some ambiguity here. That being said, the reason the integral of the HB correlation function C(t) isn't an ideal definition is that C(t) is only roughly exponential. Same argument goes for getting the lifetime from a fit to C(t), or looking for the time where C(t)=1/e, or similar simple approximations.</div><div><br></div><div>What Luzar recommends is to think about an equilibrium between bound and unbound molecules, so that they interact with a forward and a backward rate constant k and k'. k gives the forward rate, ie. the HB breaking rate, and k' gives the HB reformation rate... they are not equal due to the diffusion of unbound molecules away from the solvation shell. There are a few advantages of going this route, not the least of which is that you tend to get similar lifetimes regardless of small changes in the HB definition, and whether you use geometric or energetic criteria, etc.</div><div><br></div><div>Extracting these rate constants is a bit tricky (I usually do it by hand), but I guess gromacs has a scheme to do it... I haven't actually looked at it (though I really should!). I'd recommend some caution though, a scheme that works well for HB's between water molecules in bulk may need to be adjusted to properly model HB's between water and polar atoms.</div><div><br></div><div>So in this case, the "best" rate constant is probably 0.797 ps-1 or a time of 1.254 ps, which is only a bit slower than in bulk water. I'm very surprised that the backward rate constant is so small though... this is about 1 ps-1 in bulk water! I've never seen k' be this small...</div><div><br></div><div>Exhaustive details about the HB dynamics issues can be found eg. here:</div><div><br></div><div>A. Luzar, JCP 113, 10663 (2000)</div><div><br></div><div>Hope this helps,</div><div>Chris Daub</div><div>(currently postdoc with Dr. Luzar).</div></div></body></html>