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

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Tue Dec 1 17:33:03 CET 2009

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.


Quoting t.peter.Mueller at 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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