[gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

[Ran Friedman]

Dear Jenny,

You can do this directly in VMD, using the Periodic tab under
Graphics->Representations.

Ran

Jennifer Williams wrote:
>
>
> Hello,
>
> I am trying to find a way around a visualisation problem I am having
> in VMD. Some of my molecules go over periodic boundary conditions
> meaning that bonds sometimes appear missing when looking at movies (I
> am trying to fix this using wrap, unwrap and join in VMD but as yet no
> luck).
>
> I was wondering if there is a way in gromacs to multiply the number of
> unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the
> new unit cell to be 2x2x2. This would mean the section of the
> structure I want to zoom in doesn't go over the pbc.
>
> For the confout.gro file I have done this using
>
> genconf -nbox 2 2 2 -f confout.gro -o confbig.out
>
> and this enables me to at least see a static image where all bonds are
> present.
>
> but in order to view a movie, I need to carry out something similar on
> the traj.xtc file. I have seen that with trjconv there is the option
>
> -box  Size for new cubic box
>
> but my unit cell is not cubic, it is a parallelepiped. The cell
> dimensions are :
>
> 4.64210   3.77847   1.89596   0.00000   0.00000  -2.18150   0.00000  
> 0.00000   0.00000
>
> I tried using this anyway with the following command:
>
> trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc
>
> but the resulting .xtc file wouldn't load into VMD so I assume that
> the .xtc file and the .gro file didn't match.
>
> Any ideas?,
>
> Thanks
>
> Jenny
>
>
>
>
>
>
>
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