[gmx-users] negative HB lifetime

[Erik Marklund]

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 <benrezkallah at 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 --- -------- --------
> -- 
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