[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Erik Marklund]

Dear Apramita,

IIRC, the time is set to.-666 when gmx hbond fails to fit the kinetic model to the data. Not the most informative way of indicating an error perhaps.

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 29 Aug 2017, at 07:20, Apramita Chand <apramita.chand at gmail.com<mailto:apramita.chand at gmail.com>> wrote:

Dear All,
I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
40000 -e 100000 as options. The results came as









*ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) =
2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =     2.8733Q
=          0--------------------------------------------------Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward        -0.008
-126.851    -666.000      2.8733*

(This came for both with and without pbc). I also tried to do it from the
g_hbond command itself by giving starting time as 40ns and ending as 100ns,
but again it came negative lifetime.


Next, 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 ,1) why do the truncated trajectories give negative values
for my simulation?*



*2)If I take the whole 100ns for analysis of hydrogen bond lifetime, 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
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