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

Jennifer Williams Jennifer.Williams at ed.ac.uk
Tue Dec 8 19:36:25 CET 2009

Hi Justin

Thanks for the suggestions. However, I don't really want to stop the  
molecule moving into the next image-I start off with an alkyl chain  
where a large portion of the structure overlaps the pbc.

i.e C1-C2-C3 \\ C4-C5-C6

where || is the unit cell boundary. To see the whole alkyl chain I use  
the graphics/representations/periodic tab in VMD. The problem is that  
VMD will not allow me to draw a bond between C3 and C4 meaning I get  
odd looking movies. VMD prefers to join the C3 to the C4 in the same  
unit cell rather than the C4 sitting right next to it on the other  
side of the pbc. This means long bonds stretching the length of my  
unit cell and missing bonds between atoms sitting next to each other!  
I have spent a while trying to solve this and have posted to the VMD  
forum (as it is actually a problem with VMD and not gromacs).

If I could somehow do the same thing to the traj.xtc as I did to  
confgro.out using genconf -nbox 2 2 2 that would solve my  
visualisation problem. Do you know of a way to do this? Even a  
round-about way?  I suppose if I dumped each frame in the trajectory  
as a pdb, used genbox on them to get a 2x2x2 box and then somehow  
stuck them together into an .xtc this might work (but any suggestions  
which are less messy are greatly appreciated!)


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> 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
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
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