[gmx-users] Change PBC box size after simulation.

[Mark Abraham]

Hi,

What property do you want to make true? Does your input to trjconv -s have
it?

Mark

On Fri., 25 Jan. 2019, 10:37 Max Adamyan, <max.adamyan at gmail.com> wrote:

> Hi. After simulation, I have trajectory file with broken and jumping atoms.
> I've fixed broken atoms, and some of jumping, but no-meter how hard I try,
> I cannot get rid of all of it. I've read Gromacs suggested workflow
> <
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> to
> fix it like 100 times. I've tried literally every `gmx trjconv` options
> (and chains of options), with no success. At this point I think that my
> System is transforming in such way, that it just cannot fit inside PBC box.
> Can this be the case? If so, can I make my PBC box bigger in z direction?
> Or maybe there is some other way to fix it?
>
> --
> Sincerely,
>     Max Adamyan
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