[gmx-users] g_mindist periodic boundary condition

[Mark Abraham]

On 4/03/2010 11:30 AM, Dian Jiao wrote:
> Hi Gromacs users,
>
> I was trying to compute minimum distance between groups in a cubic water
> box with g_mindist using periodic boundary condition. In order to test
> this, I added one more "atom" which is far away from any of the other
> atoms in the pdb file. The mindist between that atom and all the waters
> were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,
> right?)

You haven't said how big your box is, or how far "far away" is, so we 
can't tell whether you think 3nm is too big, too small, etc.

> The manual shows that pbc is one of the option of g_mindist, but isn't
> the default "yes"? I even tried with "-pbc" in the command, still did
> not work. Can anyone tell me how to turn on PBC in g_mindist?

See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.

Mark