[gmx-users] Hbond-ETH-WATER

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 14:28:17 CEST 2012

On 9/18/12 8:08 AM, Praveen Kumar Sappidi wrote:
> Hi all
>   Am Simulating Ethanol-water system using Gromacs4.0.7
>   the problem is am not able to calculate number of hydrogen bonds in ethanol
> and water-ethanol.
>   i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
> see hydrogen bonding is formed
>    am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg
>   please help if anyone knows the solution

You haven't described why the above command failed to produce what you wanted. 
g_hbond should prompt you to choose groups, which should include ethanol and 
water, so you can create plots of ethanol-ethanol, water-water, and 
ethanol-water hydrogen bonds.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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