[gmx-users] Minimum distance periodic images, protein simulation

[Arun Sharma]

Hello,
I ran a 100-ns long simulation of a small protein (trp-cage) at an elevated temperature. I analysed the distance between periodic images using

g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi 

The output shows that there are situations when the closest distance between certain atoms is much lesser than 1 nm. Conventional wisdom says that if this happens the simulation results are questionable. Is this completely true? If this is indeed true, how would I ensure that this does not happen again? 

I have posted the output of g_mindist at http://postimg.org/image/bnc0ej3nb/

Any comments and clarifications are highly appreciated

Thanks,