[gmx-users] Minimum distance between periodic images

Nidhi Katyal nidhikatyal1989 at gmail.com
Tue Oct 22 11:14:55 CEST 2013

Dear all users

I have simulated a protein with two chains (153 residues each) for
50ns(restarting crashed run 3 times) using a cubic box with each side as
11nm. After finding the closest distance between the periodic images, I
found that the closest distance  becomes lesser than 1 after 23ns for few
ns and then again  shoots up (and fluctuates around the previous value) and
then again becomes lesser than 1 around 49ns.The command which I used:
g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg

Similar trend is seen when I plotted rmsd curve and distance between the
two chains or any other analysis curve (ie at those specific time intervals
in between, the value shoots up)

My question is : Will it be reasonable enough to carry out my analysis for
first 22ns and discard the rest? Is this the problem due to smaller box
size or some other parameter as the previous studies (through literature
survey) have used even much lesser box length (although their simulations
were also of short duration than 50ns).

I have posted the output of minimum distance between periodic images at :
and rmsd wrt c alpha at :


Please help me figure out the problem.
Thanks in advance.

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