[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
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 listgmx-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
Re: [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
1ns is rather an eyeblink, and MD is chaotic... what is your evidence that the trend of RMSD either run is representative? Mark On Fri, Aug 2, 2013 at 5:50 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 listgmx-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 listgmx-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
Re: [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
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.frwrote: 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 listgmx-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 listgmx-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
