Hi, are you referring to the MSD of the protein? I am not sure which of the MSDs are right, or why there is a difference between the two versions. But, both of the MSDs are plausible. There is no obvious wrong answer. Complex molecules have a long time relaxation and may exhibit glassy behavior and thus an MSD like the blue line. Look at this reference which shows that lipids exhibit sub-diffusive behavior till 30 ns. Protein dynamics are never straightforward. http://pre.aps.org/abstract/PRE/v79/i1/e011907 There is a valid issue about the discrepancy between the two versions. Others may be able to help you here. I suggest longer simulations.
On Fri, Aug 2, 2013 at 9:20 PM, Guillaume Chevrot <gchev...@cnrs-orleans.fr>wrote: > Hi, > > I performed 2 simulations of a lysozyme in water: one with the version 4.5 > of Gromacs and another with the version 4.6.1 (I used the exact same > inputs). > > Then I calculated the MSD and I obtained a complete different behavior with > the version 4.6.1 of Gromacs and this MSD is obviously wrong. > <http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg> > > Do you have any ideas what I am doing wrong or did you encounter such a > behavior? > > Regards, > > Guillaume > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
