Dear Justin, I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A, Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Comput Biol 6(10): e1000964. doi:10.1371/journal.pcbi.1000964), where the authors have clearly described the fitting of 2D diffusion coefficient to the surface lipids (diffusion along the lipid-water interface ) and 3D diffusion coefficient to the core lipids.
On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/13/13 12:20 AM, Venkat Reddy wrote: > >> Dear Justin and Piggot, >> Thanks for the suggestions. Actually, I have constructed a CG lipid >> vesicle >> by placing lipids in random conformation in a simulation box. My lipid >> system is heterogeneous, i.e., it has different types of lipids >> (POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of >> vesicle (POPC), and some stay in the intermediate region (CHOL). So, I >> want >> to calculate the diffusion rates of these lipids. Since POPC forms the >> surface (polar heads interacting with water and their tails points to the >> core), I suppose we have to calculate 2D diffusion for POPC. For the >> lipids >> in the core, they can diffuse in 3-dimension. So, it requires a 3D >> diffusion coefficient for these core lipids. How to calculate 2D and 3D >> diffusion coeff.? Hope I am clear. >> >> > 2D diffusion coefficients are what the -lateral option does. I really > don't understand why you want a 2D value for anything with spherical > symmetry. If there is an outer layer of a vesicle, that's as much a sphere > as anything inside it. > > -Justin > > > >> On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot <t.pig...@soton.ac.uk >> >wrote: >> >> Hi Venkat, >>> >>> Can you make it a bit clearer what you actually want? >>> >>> If it is the diffusion of the lipids along the curved surface of the >>> vesicle, rather than simply the overall 3D diffusion, this is not trivial >>> to calculate as I don't believe g_msd will do this for you. This property >>> has been studied before though, so I suggest you search the literature >>> for >>> papers simulating vesicles to see how the lipid diffusion was calculated. >>> >>> Cheers >>> >>> Tom >>> >>> >>> On 11/12/2013 06:35 PM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 11/12/13 1:33 PM, Venkat Reddy wrote: >>>> >>>> Thanks Justin. So, I have to calculate diffusion coefficient three >>>>> times >>>>> (x,y,z) and finally add-up together to get in 3D??? >>>>> >>>>> >>>>> If you just want the overall diffusion constant, that's what g_msd >>>> does >>>> without any additional options. >>>> >>>> -Justin >>>> >>>> >>>> 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> -- >>> Dr Thomas Piggot >>> University of Southampton, UK. >>> >>> >>> -- >>> 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