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

Erik Marklund erik.marklund at kemi.uu.se
Tue Aug 29 10:09:35 CEST 2017

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 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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