Problem encountered when running the Umbrella sampling tutorial by Justin

User discussions
1

Command line:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr
GROMACS version: version 2022.4
GROMACS modification: No
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When I followed Justin’s Gromacs tutorial of umbrella sampling, I encountered the following errors. So what should I look for
WARNING 1 [file topol.top, line 56]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES_B
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro

WARNING 2 [file topol.top, line 56]:
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
GROMACS can not reproduce properties with the GROMOS force fields - Redmine #2884 (#2884) · Issues · GROMACS / GROMACS · GitLab, and a longer
explanation of our decision to remove physically incorrect algorithms can
be found at On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .

Program: gmx grompp, version 2022.4
Source file: src/gromacs/gmxpreprocess/readir.cpp (line 3077)

Fatal error:
Group Chain_A referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.

2

Also, I checked the index.ndx file, which was generated from the following command:

gmx make_ndx -f npt.gro
...
 > r 1-27
 > name 19 Chain_A
 > r 28-54
 > name 20 Chain_B
 > q

But still “Chain_A” was not found in the index.ndx file.
So does anyone know what is going on? Thank you.

3

Hello guys, I found gromacs-2021 is free of the problem I encountered. It’s probably due to the bug in the “gmx make_ndx” command.

4

The other issues are also version-specific. Note that the tutorial is designed for 2018.x versions and does explicitly state that use of different versions may lead to problems. There are some additional checks in newer versions that don’t necessarily mean anything is wrong, but that are meant to inform you about syntactical and force field issues.

5

Thanks a lot Justin. Great tutorial by the way.

6

Hello, I encountered the same error, when following Umbrella sampling tutorial by Justin with Gromacs version2023. I am beginner user. How do you fix the issue.
Thank you.