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

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 2 04:36:37 CET 2009

t.peter.Mueller at gmx.net wrote:
> 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.

Was this .pdb file a product of a Gromacs utility?  If so, it will be of 
interest in case there needs to be a fix.  If not, it would still also be nice 
to know what lines were confusing g_mindist so others who search for this 
problem might find the solution :)


> Thanks for your feedback Peter


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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