Dear David,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes it is DGact.<br>
The DGeq follows from the fraction of COOH that are not forming hydrogen bonds, option -nhbdist.</blockquote><div> <br>So, I need to use the equation (9) and (10) from your paper to calculate the equilibrium constant and free energy of H-bonding.<br>
<br>
</div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Another question I have is, for a polycarboxylic acid system in water<br>
(COOH groups as side chains) for a 10ns run, I got the following as the<br>
output where the life time of the H-bond (between the polyacid and<br>
water) is negative. Is this correct?<br>
</blockquote></div>
This means that the ACF has not equilibrated and you need much longer sims. You probably got a warning about it.</blockquote><div class="im"> <br>I did not get a warning here. I also have simulations (20ns) of copolyacids where again it gave me negative life time. These runs are well equilibrated with respect to energy and Rg of the polymers. The system is a 20 repeat unit chain in approx. 5500 water molecules. I have done simulations in which 10 units are COO- and the remaining 10 as COOH along the chain. With a 10ns trajectory, the average life time of H-bonds is positive.Only in the case of unionized acid I am getting a negative life time.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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>
--------------------------------------------------<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<br>
<br>
<br>
</blockquote>
<br>
<br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
-- <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>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
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</font></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">What is the value for free energy of H-bonding.<br>
</blockquote></div><br>