[gmx-users] negative HB lifetime

[Benrezkallah Djamila]

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 --- -------- --------