Then, how to mention the direction for spherical particles Sir?
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/12/13 8:55 AM, Venkat Reddy wrote: > >> Thank you sir for the prompt reply. >> *g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns* >> >> Here I am giving -lateral z (like for membrane simulations). Is it fine >> for >> spherical systems also? >> >> >> > No. The system is a sphere, so what use is it to calculate motion > perpendicular to z when you have lipids moving in all three spatial > dimensions? A vesicle is very different from a membrane, in which the > lipids move in a plane, thus making "-lateral z" useful. > > -Justin > > > On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban <vvcha...@gmail.com >> >wrote: >> >> MSD is 3D by default. >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> >>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat...@gmail.com> >>> wrote: >>> >>>> Dear all, >>>> I am simulating a spherical lipid vesicle. I want to calculate the >>>> diffusion coefficient for each lipid component in 3D. How to calculate >>>> it >>>> using g_msd (or any other tool like g_velacc)? >>>> >>>> Thank you for your concern >>>> >>>> -- >>>> With Best Wishes >>>> Venkat Reddy Chirasani >>>> -- >>>> 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 >>>> >>> -- >>> 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 >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
