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 g_hbond -f traj.xtc -s traj.tpr -n index.ndx -ac and chose the polyacid and the water as the two groups.
ACF 22057/22057 Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0146697 Q = 0 ------------------------------ -------------------- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward -0.271 -3.687 -666.000 0.0146697 Backward -2.291 -0.437 -666.000 One-way 0.101 9.882 10.207 Integral 0.034 29.376 12.907 Relaxation 0.063 15.803 11.370 Thankyou for any help, Dr. M. S. Sulatha Dept. of Chemical Engineering IIT-Madras India On Tue, Dec 13, 2011 at 10:12 AM, sulatha M. S <mssula...@gmail.com> wrote: > > > 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. >>> >>> Did you look at the ACF graph? It could be constant at 1 or 0. >> > > Yes, the ACF decays to 0 and remains constant in all cases > > > >> >>> >>> Thankyou for any help, >>> >>> Dr. M. S. Sulatha >>> Dept. of Chemical Engineering >>> IIT-Madras >>> India >>> >>> >>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >>> >>> http://folding.bmc.uu.se >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> What is the value for free energy of H-bonding. >>> >>> >>> >>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >
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