[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Daer Justin

I studied your tutorial (Umbrella Sampling). It is very beneficial for me.

The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.

You considered following parameters:

Chain_B: reference group for pulling.
Chain_A: group to which pulling force is applied.
pulling direction was Z.

you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775)
in a box of dimensions 6.560 x 4.362 x 12 by editconf:

editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560
4.362 12.

I have a question:

You said " pull distance must always be less than one-half the length of
the box vector along which the pulling is being conducted".You pulled a
total distance of 5.0 nm in a 12.0-nm box, to avoid the complications
described above.

Why did you used 2.4775? I think 5.0 is true. Please give me more
explanation. How did you obtained this value?

Best wishes