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

t.peter.Mueller at gmx.net t.peter.Mueller at gmx.net
Mon Nov 30 23:28:54 CET 2009

Dear Gromacs users,

my system consist of two parts, which are not connected. My system has around 100000 atoms. To make the trajectory handling and the analysis more feasible I store only the CA atoms in the xtc trajectory.

I want to use the "g_mindist" command to calculate the minimal distance between the two parts of my system from the xtc trajectory. I created a index file, where I added the atoms of each parts of my system.

   $ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx
   $ g_mindist -f system_all.xtc -s system_all.pdb -n system_all.ndx

If I calculate the minimal distance from the XTC trajectory which contains only the CA atoms I get a too small values (much smaller then 1 Aengstroem).
For testing I calculated the minimal distance from a small part of the XTC trajectory which contains all atoms I get the correct value (around 100 Aengstroem).

What is the reason for this error? It should not matter if the trajectory has all atoms (connected via bonds) or only the CA (not connected). "g_mindist" has two sets of atoms. It will calculate the distance between all possible pairs of atoms from both groups. For every frame it will give out the smallest distance.
If there are broken molecules in the trajectory file (trajectory only CA) should not have any influence on the result.

Thanks for answering
Sarah Kreuz, die DSDS-Siegerin der Herzen, mit ihrem eindrucksvollen           
Debütalbum "One Moment in Time". http://portal.gmx.net/de/go/musik

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