[gmx-users] Minimum distance between periodic images

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 22 11:18:30 CEST 2013

Hi Nidhi,

These are periodicity artifacts. Make sure that you remove jumps over PBC
from your trajectory by using trjconv -pbc nojump.



On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal <nidhikatyal1989 at gmail.com>wrote:

> 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
> -pi
> 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 :
> https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE
> and rmsd wrt c alpha at :
> https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA
> Please help me figure out the problem.
> Thanks in advance.
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Tsjerk A. Wassenaar, Ph.D.

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