[gmx-users] g_hbond (v 3.14) vs g_hbond (3.3)

Anil Kumar anil at chem.iitb.ac.in
Fri Dec 14 07:05:23 CET 2007

Dear Users,

I have done clustering of equilibrium ensemble of octa-alanine model
system, and when i was trying to find the no. of hydrogen bonds for each
cluster, i found different result with different versions.

Is there some bug to version 3.3 in comparison of version 3.14 or am i
doing the wrong way. Please guide me.

I have used the command

g_hbond_mpi -f *.pdb -s *.tpr -num hbnum.xvg -hx hbhelix.xvg -r 0.35 -a 30

n-n	n-n+1	n-n+2	n-n+3	n-n+4	n-n+5	n-n>6
0	0	73	180	277	1036	1856	3422	Cut-off	r=0.35	a=30	v3.14
0	0	330	243	358	1382	2170	4483	Cut-off	r=0.35	a=60	v3.14
1225	2373	404	0	0	0	0	4002	Cut-off	r=0.35	a=30	v3.3

PS: In version 3.14 the default is r = 0.35 and a = 60
 and in version 3.3 the default is r = 0.35 and a = 30

My worry is that when i did calculation with v 3.3 i got more no of n-n
n-n+1 and n-n+2 hydrogen bonds, while on the same system with v 3.14 i
found 0(Zero) value for n-n n-n+1 and n-n+2 (Quite Surprising with v3.3!)

How come hydrogen bond between n-n is possible, when structures and
everything is fine.

Thanks in advance,
With Regards

ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Ph. No.-022-25764780(Lab)
Hostel#1,Room#297,IIT Bombay,Powai,
Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile)
"Education is a progressive discovery of our ignorance"

- Will Durant

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