Tutorial of sample umbrella

User discussions
1

GROMACS version:2020.1
GROMACS modification: No
I was learning this tutorial:

Umbrella Sampling.

[quote=“Gray, post:1, topic:1494, full:true”]
GROMACS version:2020.1
GROMACS modification: No
I was learning this tutorial:

Umbrella Sampling.

When I did this step:

gmx grompp -f npt_umbrella.mdp -c conf6.gro -p topol.top -r conf6.gro -n index.ndx -o npt0.tpr
…
gmx grompp -f npt_umbrella.mdp -c conf449.gro -p topol.top -r conf449.gro -n index.ndx -o npt22.tpr

I got this error:

When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.

Maybe I should expand the size of the cell, but why the tutorial doesn’t exist this problem?
Thanks for the advice of you.

2

Hello？

3

Try to reproduce the tutorial using the GROMACS version for which it is designed, 2018. There may be differences in 2020 and I haven’t had time to look into what those might be.

Please don’t do this. The users of this forum give of their free time (what is that?) to help others. It may take a few hours or even a few days for someone to provide input.

4

Thank you for your advice. I will try it.

Sorry, my apologize.I won’t do this again.