Yes, mdrun applies PBC at every step and some atoms at top/bottom will translate to the bottom/top at some steps. So in dynamics simulation, the polarization given by gromacs is meaningless. Is there anyway I can apply PBC without translation ( e.g. change the box center automatically to avoid translation) ? Thanks, Shuangxing Dai
On Wed, Jul 28, 2010 at 11:46 AM, Vitaly Chaban <[email protected]> wrote: > 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 > > > > >
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