[gmx-users] about comm_mode
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Wed Jun 19 17:19:13 CEST 2002
I still have some doubts about comm_mode options and how it works.
We are running a micelle (DPC) in a box, so comm_mode = Linear.
When using this, it seems gmx will remove center mass translation to the
whole system (micelle+water), unless I set, f.ex., comm_grps = DPC. Thus,
not defining a specific group would explain why we see our micelle
traveling around the box (some DPC crossing the box), right? And so,
defining comm_grps = DPC should give us the micelle in the middle of the
box, shouldn't it?
Anyway, since we have already done a long simulation with
comm_grps taking the whole system and thus with our micelle sometimes
crossing the box, we tried to use trjconv to center the micelle in the box
but no options worked. We tried '-pbc none' (to remove periodicity), but
Is gmx writing the atoms coordinates translated to the box in the
xtc file during the simulation?
Could someone give a light to us about it? Many thanks in
Alan Wilter S. da Silva
Laboratório de Física Biológica
Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
Rio de Janeiro, Brasil
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