Change of Simulation Box shape

User discussions
1

GROMACS version:2020
GROMACS modification: Yes/No
Here post your question

Hi all,

I am currently running a long simulation but I would like to change the box shape (From triclinic to cubic) . Can I finish this simulation and then change the box shape and continue the simulation from the current time point to continue the run or I need to start from time 0?. Is there any GROMASC option I can use to change the dimension of the box from triclinic to a cubic or orthorhombic box? Any suggestions would be highly appreciated.

Thank you so much

Amnah

2

Hi,
usually reshaping a box may require also partial re-solvation of the box and a change in the phase space, thus the simulation will start from t=0.
Then in the analyze you can consider both simulation separately.
Best regards
Alessandra

3

@alevilla
Thank you so much Alessandra for replying!
The problem is I already ran the simulation for 2us which took us so long! so there is no way to continue the simulation from the last time point after re-shaping the box?

I have been advised to use the following commands :
gmx editconf -f your_system.gro -o new_cubic_system.gro -bt cubic
then
grompp specifying
-c new_cubic_system.gro -r new_cubic_system.gro -t previous_geometry_checkpoint.cpt

Any suggestions would be greatly appreciated.

Amnah