[gmx-users] Handling Periodic Boundary Conditions

[Lovas, Sandor]

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
Sandor


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