Why is my collective variable negative during metadynamics?

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1

GROMACS version:2022.4
GROMACS modification: Yes/No
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Hi all.
I am carrying out a metadynamics simulation where my collective variable is distance between two groups. The FES I’m getting in some case has values in negative for the x-axis, i.e the collective variable. Can anyone tell me if I’m doing it wrong and how to correct it ?

2

Hi,

Did you visually inspect what happens during your simulation at these negative values? It could be that your “distance” C.V. is directional, so once your two groups cross paths on the x-axis you start getting negative values.

3

I looked into the COLVAR file. There is no such negative values for the CV. But the FES I am getting has some initial values in negative. I visualized the trajectory file. There is nothing abnormal about it.