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

[herbst at fhi-berlin.mpg.de]

> 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.
>
Pressure coupling was switched off, so the box size should have remained
constant. In trjconv I only used -center and -pbc whole. That does not
change it as well, does it? And the box size was already wrong before I
used trjconv. Is there anything else that could change the box size? In
ngmx is was much too big already in the beginning and the size did not
change later.  But genbox always fills the whole box with water, doesn`t
it?
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| 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           |
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