[gmx-users] g_mindist , trajectory only CA atoms, to small values?

t.peter.Mueller at gmx.net t.peter.Mueller at gmx.net
Wed Dec 2 03:19:20 CET 2009

Dear Shay, dear Justin, dear Gromacians

My problem is solved. I used following command   

$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o atm-pair.out 

The PDB file "system_onlyCa.pdb" had a header which seems to have confused the counting of the "g_mindist" command. After deleting the the PDB header/ comments, I get the correct results.

Thanks for your feedback
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