[gmx-users] under boundary to box size or ngmx-problem?

Anton Feenstra feenstra at chem.vu.nl
Tue Aug 17 17:47:40 CEST 2004

herbst at fhi-berlin.mpg.de wrote:
> Hi Nuno,
> using trjconv centers my solute molecule in the box, but the solvent still
> moves out of my defined box, so it does not really help me. The problem is
> that ngmx uses a larger box than I defined for the simulation. In the
> beginning, all molecules are in the small box I defined. In fact I just
> want to know whether in the gromacs simulation, the small box is used and
> ngmx just does not display it right or whether I somehow defined the box
> wrong and only a small part of it is filled with water?

ngmx will show the box exactly as it is stored in the trajectory file.
Your box may have grown during simulation due to pressure coupling.
There is no requirement per se for all molecules or atoms to be inside
the box at any time. In fact, mdrun will keep all molecules whole, so
parts of molecules will stick out of the box at any time. However, trjconv
has several options to rearrange atoms, e.g. all atoms in the box, or the
system as compact as possible (option -pbc). Finally, trjconv has also an
option to *set* the *box* *size* in the output trajectory (while not changing
anything per se about the atomic coordinates). If you did that, obviously
ngmx will show that new box.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

More information about the gromacs.org_gmx-users mailing list