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