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

[Justin A. Lemkul]

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.
> 

Correcting periodicity should alleviate some of the problems.  Using trjconv 
-pbc mol (or -pbc nojump) is typically the best first step.

-Justin

> Any ideas?,
> 
> Thanks
> 
> Jenny
> 
> 
> 
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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