[gmx-users] Gromacs 3D maps

[Mark Abraham]

On 18/11/2011 12:24 AM, Alex wrote:
> Dear all,
>
> I'd like to transform an md gromacs trajectory in a 3d maps set.
> I mean that every 100ps, I need to export frame coordinates to a 3d map.
> Than I need to compare a map with the following.
> Could give me any advice about tools/software to use?

I don't know what you mean by a 3d map.

> Additionally I need to export the coordinate (x,y,z) of atom's protein, deriving
> from MD trajectory, to a matrix where each columns are frame number, 1-n
> atoms'positions (x,y,z coordinates).
> Any suggestion?
>

Check out manual section 7.4 for clues on what the tools do, then the 
appropriate appendix section for more details. g_traj sounds like a good 
place to start.

Mark