Hi Shuangxing, For my case, I wrote a script just to do +/- LBOX when x>LBOX || x < 0. I am not well familiar with polarization algorithm in gromacs but it seems not to be a problem during a run since mdrun applies PBC at every step. Maybe I am false here...
Vitaly On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai <[email protected]> wrote: > I think I met the same problem. When apply periodicity to the system, some > atoms will translate to the other side of the box, and this gives wrong > polarization values (especially in dynamic simulations). Anyone has idea how > to prevent this and get correct polarization in dynamics? > Thanks, > Shuangxing Dai > > > On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban <[email protected]> wrote: >> >> Hi, >> >> Is there an option in any gromacs utility to apply periodicity to the >> output configuration or trajectory? I want to get all the coordinates >> just within an elementary box, between 0 and LBOX in spite of any >> details of the system. >> >> For example, "editconf -no(pbc)" does not do its work since after >> processing negative coordinates are sometimes present as well as those >> bigger than LBOX. >> >> Vitaly >> >> Dr. Vitaly Chaban >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
