Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the box, then running g_msd on the results. Perhaps you'll have some more success with that workflow.
Cheers, Matt Z. On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi <[email protected]> wrote: > 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 <[email protected]> > Date: Fri, Dec 9, 2011 at 12:17 AM > Subject: Comment for Forum topic: diffusion coefficient > To: [email protected] > > > 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 [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... >> [2] >> >> >> Mark > > Read more > 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 You can > unsubscribe at > http://support.scalalife.eu/notifications/unsubscribe/sid/131?signature=c1e841f7c725c82291ca5d3191044f3c > > > [1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant > [2] > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > > > -- > Best, > Ruhollah Moussavi-Baygi > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
