[gmx-users] How to choose bd_fric value in brownian dynamics
Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply in advance, Mohan -- 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] How to choose bd_fric value in brownian dynamics
According to my understanding, setting friction coefficient is quite a personal thing. The higher is bd-fric, the smaller are velocities. Why not to set bd-fric = 0 in order to start with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply in advance, Mohan -- 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] How to choose bd_fric value in brownian dynamics
Hello Sir , Thanks for your quick reply. I have used bd_fric =0 and then my simulation is blowing up. I have used a time step of 0.002ps, Hence i thought if i can use some other value rather than zero but I do not know which value to use. Can you suggest any general value for protein water simulations. Thanks, Mohan On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: According to my understanding, setting friction coefficient is quite a personal thing. The higher is bd-fric, the smaller are velocities. Why not to set bd-fric = 0 in order to start with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply in advance, Mohan -- 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 -- 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] How to choose bd_fric value in brownian dynamics
Hello Mohan - I do not use Brownian dynamics code routinely to have exact values for various cases, but if I were you, I would start with smaller value and then increase, until your simulation runs fine. The time-step depends not on the method, but on characteristic oscillations (bond lengths, etc) in your system, so maybe 2fs is just too much for your case. Although one, in principle, can scale the force and apply a large time-step, it will not bring any performance gain at the very end. It is my impression that there are very few people in the community, who use BD engine in GROMACS. Why don't you want to use molecular dynamics? Dr. Vitaly Chaban On Wed, May 29, 2013 at 4:10 PM, Mohan maruthi sena maruthi.s...@gmail.comwrote: Hello Sir , Thanks for your quick reply. I have used bd_fric =0 and then my simulation is blowing up. I have used a time step of 0.002ps, Hence i thought if i can use some other value rather than zero but I do not know which value to use. Can you suggest any general value for protein water simulations. Thanks, Mohan On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: According to my understanding, setting friction coefficient is quite a personal thing. The higher is bd-fric, the smaller are velocities. Why not to set bd-fric = 0 in order to start with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply in advance, Mohan -- 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 -- 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
