Umbrella sampling box size error

User discussions
1

Hello Everyone,

I am trying to run my peptide for umbrella sampling. Pulling in the Z direction.

Box size is below

gmx editconf -f seq1.X.gro -o seq1.X-newbox.gro -center 3.280 3.281 5.7965 -box 6.41840 6.44350 8.7965

gmx editconf -f seq1.X.gro -o seq1.X-newbox.gro -center 3.280 3.281 5.7965 -box 6.41840 6.44350 10.7965

I do not know why I am getting the same message even I changed my box Z coordinate from 8.7965 to 10.7965. Any Suggestion.

Distance between pull groups 1 and 2 (3.475811 nm) is larger than 0.49 times the box size (3.475776).

Distance between pull groups 1 and 2 (3.409405 nm) is larger than 0.49 times
the box size (3.409306).

2

Hi,

When the box size is compared with the distance, the smaller size is of the box considered. It is a guess from the information that you reported.

\Alessandra