[gmx-users] Minimum distance between periodic images

[Nidhi Katyal]

Thank you sir.


On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Nidhi,
>
> These are periodicity artifacts. Make sure that you remove jumps over PBC
> from your trajectory by using trjconv -pbc nojump.
>
> Cheers,
>
> Tsjerk
>
>
> 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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