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 <nidhikatyal1...@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. > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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