Dear gromacs users, I have a question regarding the hydrogen bonding energy calculation. I am trying to reproduce hydrogen bonding energy in David’s paper from J. Phys. Chem. B 2006, 110, 4393-4398.
I set up my systems using OPLS force field, with TIP3P, SPC and SPCE water models. My systems just contain water molecules. The results I got for tip3p are as follows: Doing autocorrelation according to the theory of Luzar and Chandler. Normalization for c(t) = 0.000585267 for gh(t) = 2.92622e-08 Hydrogen bond thermodynamics at T = 298.15 K Fitting parameters chi^2 = 0.0139988 Q = 0 -------------------------------------------------- Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 0.534 1.873 6.083 0.0139988 Backward 0.632 1.583 5.667 One-way 0.605 1.652 5.773 Integral 0.326 3.070 7.309 Relaxation 0.534 1.871 6.081 where I think 6.083 kJ/mol is the activation energy for hydrogen bonding. However this value is much larger than 3.95 kJ/mol as in the 2006 JPCB paper. A few questions that I have are: 1. Does the version of gromacs matters? In the paper, GROMACS 3.3.1 was used for simulation and GRIMACES 3.3 was used for analysis. I am using GROMACS 5.0.1. 2. All the other systems parameters are set up as described in Erik’s 2003 paper in J. Chem. Phys. 119, No 14, 8, except that I use SHAKE algorithm to constrain the water molecules, they use SETTLE. Could anyone elaborate on the difference that might cause? Thanks for all your help in advance! Ben -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
