[gmx-users] No Distribution?

[Xu Dong Huang]

Dear All,

My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I execute the following: 
g_bond -f npt.xtc -n index.ndx -o bonds.xvg

I get the following error: 
Total number of samples               : 153
Mean                                  : 0.501255
Standard deviation of the distribution: 0.152864
Standard deviation of the mean        : 0.0123583

Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1#

-------------------------------------------------------
Program g_bond, VERSION 4.5.5
Source code file: gmx_bond.c, line: 207

Fatal error:
No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 
Upon inspecting my index files, I see that it defines my 3 particle group as:
[ O1 ]
   1    2    3 

Then I changed the particle group index file to 
[ O1 ]
   1    2    
   2	3
   1	3

And I’m still getting the same error. 

Any insights?

Thanks,

Xu Huang