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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to