[gmx-users] Hbond-ETH-WATER

[Justin Lemkul]

On 9/18/12 8:56 AM, Praveen Kumar Sappidi wrote:
> Hi Justin
> prompt for calculation i have shown below
>
>   Reading file eth-water60%-production.tpr, VERSION 4.0.7 (single precision)
> Note: tpx file_version 58, software version 73
> Specify 2 groups to analyze:
> Group     0 (         System) has 19412 elements
> Group     1 (           ETHH) has  7412 elements
> Group     2 (            SOL) has 12000 elements
> Group     3 (            EC1) has  1853 elements
> Group     4 (            EC2) has  1853 elements
> Group     5 (             EO) has  1853 elements
> Group     6 (             OW) has  4000 elements
> Group     7 (             EH) has  1853 elements
> Group     8 (            HW1) has  4000 elements
> Group     9 (            HW2) has  4000 elements
> Select a group: 1
> Selected 1: 'ETHH'
> Select a group: 2
> Selected 2: 'SOL'
> Checking for overlap in atoms between ETHH and SOL
> Calculating hydrogen bonds between ETHH (7412 atoms) and SOL (12000 atoms)
> Found 4000 donors and 4000 acceptors
> Reading frame       0 time    0.000
> Will do grid-seach on 15x15x15 grid, rcut=0.35
> Reading frame    2000 time 4000.000
> Average number of hbonds per timeframe 0.000 out of 8e+06 possible
>

Can you please post your topology for ethanol?  I suspect your atoms are named 
in a way that g_hbond doesn't not recognize, since the number of donors and 
acceptors seem to only correspond to water (12000/3 = 4000).

-Justin

-- 
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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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