Re: [gmx-users] trjconv with multiple chains
Make your box bigger? 2011/1/6 yuanyuan wang yilin3...@126.com dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan -- 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] trjconv with multiple chains
Amit Choubey wrote: Make your box bigger? Box size is unrelated to trjconv. Periodicity effects will still apply - things will diffuse no matter how large you try to make the box. -Justin 2011/1/6 yuanyuan wang yilin3...@126.com mailto:yilin3...@126.com dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://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] trjconv with multiple chains
On 07/01/11 02:17, yuanyuan wang wrote: dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. If they do cluster together fast (like mine), the solution I found -with the help of Justin Lemkul, if I remember correctly- was to use trjconv for simply centering on one of the chains. This way the aggregate, once formed, stayed in the center. If they just diffuse, I suspect there's nothing you can do: you have stuff diffusing in a periodic system, and WYSIWYG. m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] trjconv with multiple chains problem
dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan -- 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] trjconv with multiple chains problem
yuanyuan wang wrote: dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. Use a custom index group to center on some subset of atoms that you want to be centered in the system. If you try to just center on, for example, Protein, the geometric center may lie in the middle of the unit cell but the chains are split across periodic boundaries. -Justin yuanyuan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://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] trjconv with multiple chains
dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box, and -boxcenter, -fit .. still some chain cannot convert into box. them jump from one box to another , is there any ways that they not jump to another box? thanks a lot. yuanyuan-- 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
