Thanks Justin. So, I have to calculate diffusion coefficient three times (x,y,z) and finally add-up together to get in 3D???
On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/12/13 12:30 PM, Venkat Reddy wrote: > >> Dear Sir, Thanks for the quick reply. >> So, I have to declare -type no flag. Isn't it?? >> > > The options for the -type flag are x, y, or z. You said you wanted the > diffusion coefficient in each spatial dimension. That is precisely what > this option will do. > > > and I have recently gone through Justin's membrane protein tutorial, where >> > > You mean my tutorial :) > > > he has calculated diffusion coefficient for lipids in a membrane by >> creating an index group for a particular atom. So, here also shall I do >> the >> same thing? Moreover, mine is a coarse-grained system. >> >> > Yes, a representative atom is usually what is passed to g_msd. > > > -Justin > > >> >> On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 11/12/13 11:25 AM, Venkat Reddy wrote: >>> >>> Then, how to mention the direction for spherical particles Sir? >>>> >>>> >>>> Read g_msd -h again, paying specific attention to the -type flag. >>> >>> >>> -Justin >>> >>> >>> 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 >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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 >>> >>> >> >> >> > -- > ================================================== > > 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