On 9/20/13 4:11 PM, Arun Sharma wrote:
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?

Using a sufficiently large box (minimum solute-box distance at least equal to 
the longest cutoff) is the general procedure.
I have posted the output of g_mindist at http://postimg.org/image/bnc0ej3nb/

Some configurations definitely come very close, indicating several frames with 
spurious forces throughout the duration of the trajectory.  I would be very 
suspicious of the results.
-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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