[gmx-users] Handling Periodic Boundary Conditions

[Peter Kroon]

Hi Akash,


a cheap trick you can try (depending on your system) is to center your
trajectory on some residue or atom in the middle of your
protein/assembly/...

Otherwise it sometimes helps to invoke trjconv multiple times. First
with e.g. -pbc whole, and a second time with -center.


Peter


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