[gmx-users] Handling Periodic Boundary Conditions

Peter Kroon p.c.kroon at rug.nl
Wed Nov 22 11:27:43 CET 2017

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

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


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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