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

Max Adamyan max.adamyan at gmail.com
Fri Jan 25 10:37:31 CET 2019


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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