[gmx-users] Box dimensions in the gro file are not read by GROMACS

[Sajeewa Pemasinghe]

Hi everyone,

I have run an equilibration of two linear molecules in a water box with
dimensions 117A x 54A x 70A for 150 ns. I am using the equilibrated
structures (not the final structure) in the final nanoseconds as starting
structures for an umbrella sampling calculation. The problem is that as I
only have a checkpoint (cpt) file for the final structure I have to start
these umbrella sampling calculations without a cpt file. So my inputs to
grompp are just the .gro files. During the umbrella sampling I get the
following error

Distance between pull groups 1 and 2 (3.599998 nm) is larger than 0.49
times the box size (2.673675).
You might want to consider using "pull-geometry = direction-periodic"
instead.

Although gromacs says that the distance between the pull groups 1 and 2 are
3.599998 nm, the actual distance in the snapshot is 23.0 nm. This was
confirmed by calculating in vmd as well.
The above error also says that the box size is 2.673675 nm. But at the
bottom of the input gro file it shows the dimensions as 11.68645
5.34804   6.95245. So I cannot understand why it doesn't read those
dimensions.

I am doing this umbrella sampling in the NPT ensemble. As the gromacs
manual suggests "no-pressure scaling" for "pull-geometry =
direction-periodic" I cannot use it either.

I would highly appreciate some help with this problem.

Thank you very much

Sajeewa