[gmx-users] Re: Simulating a large system
Hi, is it possible to instruct gromacs to only perform the dynamics on half of the system or protein while ignoring the rest? thanks Would you explain to us why you need so exotic setup? Dr. Vitaly Chaban -- 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] Re: Simulating a large system
Sure, it's basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure. As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but you're moving. On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote: Vitaly Chaban -- 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] Re: Simulating a large system
If you do not care about the atoms, which are too far away from the region of interest, is it not reasonable just to cut that useless part? Also, you may want to look towards implicit solvent simulations. Dr. Vitaly Chaban On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay raygo...@psu.edu wrote: Sure, it's basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure. As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but you're moving. On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote: Vitaly Chaban -- 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] Re: Simulating a large system
On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: If you do not care about the atoms, which are too far away from the region of interest, is it not reasonable just to cut that useless part? Also, Hear hear. If it's so meaningless, why is it there? ;) you may want to look towards implicit solvent simulations. Indeed. Or use GPU's. Erik was showing us great performance on a laptop during the webinar, even using (relatively) cheap consumer-grade cards. Back to the original point (and as I posted before), even if you freeze some amount of atoms, you don't gain any performance by doing so. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: Simulating a large system
Yes, there's no way to cheat on the explicit electrostatics to reduce cost, except implicit solvation. The kind of approach used in QM/MM is not useful for MM/MM! The rate-limiting part is still there. Mark On Apr 8, 2013 12:42 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: If you do not care about the atoms, which are too far away from the region of interest, is it not reasonable just to cut that useless part? Also, Hear hear. If it's so meaningless, why is it there? ;) you may want to look towards implicit solvent simulations. Indeed. Or use GPU's. Erik was showing us great performance on a laptop during the webinar, even using (relatively) cheap consumer-grade cards. Back to the original point (and as I posted before), even if you freeze some amount of atoms, you don't gain any performance by doing so. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Aw: [gmx-users] Re: Simulating a large system
Funny, I thought of a large Ribosome system. You can in vacuo already with an i7 or AMD equivalent EM a 600 amino acid system with a 12-15A solvent shell in an hour to three using the CPU alone. Thats from test of Gromacs and a non-eqd system. so about 1 work day to get through NPT. Thus, I doubt there is much problem even using the whole system for most things if your time frame is a day or two and newer PC . Stephan Watkins Gesendet:Montag, 08. April 2013 um 11:35 Uhr Von:Juan Antonio Raygoza Garay raygo...@psu.edu An:vvcha...@gmail.com Cc:gmx-users@gromacs.org Betreff:[gmx-users] Re: Simulating a large system Sure, its basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure. As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but youre moving. On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote: Vitaly Chaban -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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
