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
