David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2nd.xvg
when visualizing, I can see that the polypeptide crosses the boundary several times. apparently, g_msd counts these 'artificial' jumps in MSD calculation. and, that's probably why the diffusion coefficient is calculated such high (i.e. 500 um2/s for a small protein). if this is the case, it is a bug in g_msd I believe. is there any way to get round this problem? ---------- Forwarded message ---------- From: Anonymous <ros...@kth.se> Date: Fri, Dec 9, 2011 at 12:17 AM Subject: Comment for Forum topic: diffusion coefficient To: ruhollah...@gmail.com Hi ruhollahmoussavi-baygi, Comment by davidvanderspoel: diffusion coefficient On 2011-12-09 08:34, Mark Abraham wrote: > On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: >> I want to calculate the diffusion coefficient of a small polypeptide >> with g_msd (see here >> http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant<http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant>[1]) >> >> because of periodic boundary condition, when the peptide goes out of >> the right side it comes in from left side, which leads to an >> artificial displacement. this will give rise to a non-realistic MSD. >> >> is g_msd intelligent enough to avoid this artificial displacement? >> > Yes it is. > Not sure about g_msd, but you can take care of it yourself with a > workflow derived from the information here > http://www.gromacs.org/**Documentation/Terminology/** Periodic_Boundary_Condi.<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi.>.. [2] > > > Mark Read more http://support.scalalife.eu/**content/diffusion-coefficient#** comment-103<http://support.scalalife.eu/content/diffusion-coefficient#comment-103> -- This is an automatic message from ScalaLife To manage your subscriptions, browse to http://support.scalalife.eu/**user/291/notifications<http://support.scalalife.eu/user/291/notifications>You can unsubscribe at http://support.scalalife.eu/**notifications/unsubscribe/sid/**131?signature= **c1e841f7c725c82291ca5d3191044f**3c<http://support.scalalife.eu/notifications/unsubscribe/sid/131?signature=c1e841f7c725c82291ca5d3191044f3c> [1] http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant<http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant> [2] http://www.gromacs.org/**Documentation/Terminology/** Periodic_Boundary_Conditions<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions> -- Best, Ruhollah Moussavi-Baygi
-- 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
