As suggested by David I extended the simulations (total of 25ns) for a single chain polyacid in 5500 water molecules and tried to calculate the H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups and water. Is it that the g_hbond ACF giving weird results for this case. For chains with COO- and COOH groups (50% each), I got positive life times of Hbond. Ayy ideas on how to solve this will be of great help. I am using 4.0.7 version. The command line I gave was<br>
g_hbond -f traj.xtc -s traj.tpr -n index.ndx -ac and chose the polyacid and the water as the two groups.<br><br><br>ACF 22057/22057<br>Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06<br>Hydrogen bond thermodynamics at T = 298.15 K<br>
Fitting parameters chi^2 = 0.0146697<br>Q = 0<br>------------------------------<div id=":2e">--------------------<br>
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2<br>Forward -0.271 -3.687 -666.000 0.0146697<br>Backward -2.291 -0.437 -666.000<br>One-way 0.101 9.882 10.207<br>Integral 0.034 29.376 12.907<br>
Relaxation 0.063 15.803 11.370<br><br><br>Thankyou for any help,<br><br>Dr. M. S. Sulatha<br>Dept. of Chemical Engineering<br>IIT-Madras<br>India</div><br><br><div class="gmail_quote">On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S <span dir="ltr"><<a href="mailto:mssulatha@gmail.com">mssulatha@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br><br><div class="gmail_quote"><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I did not get a warning here. I also have simulations (20ns) of<br>
copolyacids where again it gave me negative life time. These runs are<br>
well equilibrated with respect to energy and Rg of the polymers. The<br>
system is a 20 repeat unit chain in approx. 5500 water molecules. I have<br>
done simulations in which 10 units are COO- and the remaining 10 as COOH<br>
along the chain. With a 10ns trajectory, the average life time of<br>
H-bonds is positive.Only in the case of unionized acid I am getting a<br>
negative life time.<br>
<br>
</blockquote></div>
Did you look at the ACF graph? It could be constant at 1 or 0.<br></blockquote></div><div><br>Yes, the ACF decays to 0 and remains constant in all cases<br><br> </div><div><div></div><div class="h5"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<br>
<br>
Thankyou for any help,<br>
<br>
Dr. M. S. Sulatha<br>
Dept. of Chemical Engineering<br>
IIT-Madras<br>
India<br>
<br>
<br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br></div>
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What is the value for free energy of H-bonding.<br>
<br>
<br>
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</div></blockquote><div><div>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
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