[gmx-users] Handling Periodic Boundary Conditions

Lovas, Sandor SandorLovas at creighton.edu
Wed Nov 22 17:27:11 CET 2017

Hello Akash,

Let's assume that in your "non_water.tpr" group 1 is your protein; the following always worked for me:

1 1 1 | gmx trjconv -f Nonwater.xtc -s non_water.tpr  -pbc cluster - center -boxcenter tric

of course "-boxcenter tric" depends on your box type

On 21-11-17 21:54, Pandya, Akash wrote:

> Hi all,


> I'm having trouble with visualisation of my system after the MD production run. I have tried the periodic boundary conditions workflow suggested on the gromacs website, although I'm having no luck. I have used the following command to try and obtain a visualisation state that I can work with.


> gmx trjconv -f Nonwater.xtc -s non_water.tpr -pbc whole -center -o nonwater.gro


> When I visualised this trajectory, my protein molecule appears to have split even though I used -pbc whole. Can someone please help me overcome this issue?


> Many thanks,


> Akash

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