Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water.
I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 = 3.03095Q = 0--------------------------------------------------Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.001 1793.775 23.259 3.03095* When I tried the same with the original unconverted trajectory(without g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*. *My question is ,* *Which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.* I would be very grateful for your help. Looking forward to your suggestions Yours sincerely Apramita Chand -- 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.
