I gratefully appreciate to your reply Justin. You are right, it seems that g_msd provides the MSD.xvg file what I want (in one direction). I was confused before.
Thanks again. 2012/11/23 Justin Lemkul <jalem...@vt.edu> > > > On 11/22/12 5:44 AM, Kiwoong Kim wrote: > >> Hi, >> >> It seems that the one directional diffusion constants can be obtained by >> means of g_msd ...blabla...-type z. >> >> However, my question is that I don't want to obtain the diffusion >> constants. >> >> Actually, the MSD trajectory file for all 3 dimensional data can be >> obtained by conventional g_msd... >> Instead, I want to obtain MSD (time)trajectory file (.xvg file) that >> contain only one directional, say z, data. >> >> I want to analyze it and regress it by curve fitting from the MSD data. >> >> How can I do this ? >> >> > The only useful output file from g_msd is msd.xvg (the default output). > Does this not contain what you want? The help description seems to > suggest it does. If, for some reason, this is not the information you're > after, you'll probably have to modify the code yourself to produce the > desired output, but it seems to me that MSD will be written to msd.xvg > under the parameters (i.e. direction) you specify. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
