[gmx-users] Query about g_hbond

naimah haron naimah cimot_ima98 at yahoo.com
Wed Feb 24 05:54:22 CET 2010

Dear gmx-users...

I am new to gromacs, I am trying to obtain the intermolecular hydrogen bonds formed during 10ns simulation of 125 ionic liquid (tetraethylammonium L-Lysinate). I use OPLS-AA force field for this simulation. When I do this by using g_hbond and selecting the LYS group, I am getting hydrogen bonds at all. The angle that I get is 0.33 degree, number of hydrogen bonds = 160.13, and the distance for hydrogen bond =0.16 nm.

This is the command I am using:

g_hbond -f mixture_mdpr_compilefile.trr -s mixture_mdpr_ext1.tpr -n index.ndx -num hbnum.xvg -dist hbdist.xvg -ang hbang.xvg -hbn hbond.ndx -d 500 -e 10000 -a 30 -r 0.35 

This is the output that I obtain :

No option -sel
Reading file mixture_mdpr_ext1.tpr, VERSION 3.3.3 (double precision)
Specify 2 groups to analyze :
Group     0 (    System) has   6500 elements
Group     1 (     N2222) has   3625 elements
Group     2 (       LYS) has   2875 elements

Select a group: 2
Selected 2: 'LYS'
Select a group: 2
Selected 2: 'LYS'
Calculating hydrogen bonds in LYS (2875 atoms)
Found 250 donors and 500 acceptors 
trn version: GMX_trn_file (single precision)
Reading frame   2000 time  500.000
Will do grid-seach on 9x9x9 grid, rcut=0.35
Last frame    40000 time 10000.00
Found 2353 different hydrogen bonds in trajectory
Found 2271 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
-Reduced number of hbonds from 2353 to 1783
-Reduced number of distances from 2271 to 2271
Average number of hbonds per timeframe 160.130 out of 62500 possible

gcq#44: "May the Force Be With You" (Star Wars)

My question is; 
1) Is it correct the command that I used to get the number of hydrogen bonding, angle and distance for hydrogen bonding?
2) Is it reasonable the value for number of hydrogen bonding, angle and distance for hydrogen bonding that I calculate?



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