Re: [gmx-users] Calculating diffusion coefficient in three dimension
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.ukwrote: 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 listgmx-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 listgmx-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,
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
On 11/13/13 9:41 AM, Venkat Reddy wrote: 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 Diffusion along a lipid-water interface is one thing. Trying to use g_msd do to it is another, because I don't think it will. It looks for a plane in the configuration and calculates relative to it. I suspect you will need to modify the code to implement a custom algorithm. -Justin ) 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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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? On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
Dear Sir, Thanks for the quick reply. So, I have to declare -type no flag. Isn't it?? and I have recently gone through Justin's membrane protein tutorial, where 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. 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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 listgmx-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 listgmx-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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please
Re: [gmx-users] Calculating diffusion coefficient in three dimension
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. On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot t.pig...@soton.ac.ukwrote: 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 listgmx-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 listgmx-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
