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
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
