Hi, Did you look at the ACF? I suspect you have too noisy data so that g_hbond can't calculate the rate constants, in which case it spits out DG = -666.
Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 14 Apr 2014, at 18:46, Benrezkallah Djamila <benrezkal...@gmail.com> wrote: > Dear users, > > I try to calculate Hydrogen Bonding lifetimes with g_hbond, but I get a > negative value for the forward time. > > I searched through the mailing list, and it reports that we should look to > the ACF graph. In my case it falls dramatically to zero(I have attached it > to this mail). > > How can I get a reasonable value for the HB lifetime? > > Any suggestions are welcome, Thank you in advance. > > Djamila Benrezkallah > > > > > > > > this is my output: > > > > g_hbond -f trajpbc.xtc -s md15.tpr -n index_electro.ndx -hbn > HB52a_bb_Wat.ndx -b 1000 -e 10000 -ac -life -temp 300.15 > > > > > > Select a group: 31 > > Selected 31: 'Lys52a_bb' > > Select a group: 17 > > Selected 17: 'Water' > > Checking for overlap in atoms between Lys52a_bb and Water > > Calculating hydrogen bonds between Lys52a_bb (6 atoms) and Water (26385 > atoms) > > Found 8796 donors and 8797 acceptors > > Making hbmap structure...done. > > Reading frame 0 time 1000.000 > > Will do grid-seach on 17x17x12 grid, rcut=0.35 > > Reading frame 4000 time 9000.000 > > Found 716 different hydrogen bonds in trajectory > > Found 1014 different atom-pairs within hydrogen bonding distance > > Merging hbonds with Acceptor and Donor swapped > > 8796/8796 > > - Reduced number of hbonds from 716 to 716 > > - Reduced number of distances from 1014 to 1014 > > > > Average number of hbonds per timeframe 1.956 out of 3.86892e+07 possible > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu > > Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media > > J. Phys. Chem. B 110 (2006) pp. 4393-4398 > > -------- -------- --- Thank You --- -------- -------- > > > > Doing autocorrelation according to the theory of Luzar and Chandler. > > ACF 716/716 > > Normalization for c(t) = 0.511249 for gh(t) = 0 > > > > Hydrogen bond thermodynamics at T = 300.15 K > > Fitting parameters chi^2 = 0.00313318 > > Q = 0 > > -------------------------------------------------- > > Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 > > Forward -0.076 -13.173 -666.000 0.00313318 > > Backward -0.000 -9761.188 -666.000 > > One-way 0.052 19.251 11.956 > > Integral 0.020 50.885 14.382 > > Relaxation 0.029 34.606 13.419 > > > > > > HB lifetime = 8.13 ps > > Note that the lifetime obtained in this manner is close to useless > > Use the -ac option instead and check the Forward lifetime > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu > > Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media > > J. Phys. Chem. B 110 (2006) pp. 4393-4398 > > -------- -------- --- Thank You --- -------- -------- > -- > 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. -- 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.