GROMACS Tutorial Umbrella Sampling

User discussions
1

GROMACS version: 2021.2
GROMACS modification: Yes/No

Hello everyone, I am new to GROMACS and I am studying tutorial 3 umbrella sampling. I got some problems at the beginning of this tutorial.

  1. At the second step, I tried to use vmd to visualize the location of the protofibril within the box by the command line:

vmd > pbc box

The terminal showed the following without the image:

molinfo: get: no molecule exists with id -1

  1. I skipped this error and went to step 3 (Solvate and add ions), when I ran the following command line:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

It does not output the ions.tpr and has one warning:

The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://redmine.gromacs.org/issues/2884 , and a longer explanation of our decision to remove physically incorrect algorithms can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 .

Any reply would be appreciated!

2

I don’t have any idea about the VMD issue.

The note about the GROMOS force fields is rather well explained by the two links provided. The tutorial was designed for use with version 2018, in which no such warning exists. To complete the tutorial, you can override the warning with -maxwarn 1, but this is strongly discouraged for general use. GROMACS is simply telling you that there are issues of reproducibility with the GROMOS force field, though the discussion about the extent and severity of these issues is ongoing. The tutorial (and published paper from 2010) used GROMOS96 53a6, so you can safely ignore the warning for the purposes of reproducing the workflow, but be cautious about using GROMOS for new scientific investigations unless you fully understand the scope of the debate that is being carried out in the literature.