Thank you sir.
On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar <tsje...@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 <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 > -- 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