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

[Jennifer Williams]

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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