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

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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