Dear Peter,
For purposes of debugging this bug you can also use the flag of
g_mindist that gives out atom pairs and see which atom pairs is it
that gromacs thinks are less the 1 angstrom.
Another suggestion would be using the backbone and seeing if it matters any.
Regards,
-Shay
Quoting t.peter.muel...@gmx.net:
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
Peter
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