GROMACS 2020.3
GROMACS modification: No
I have been asked by a customer to download the rnace_bench_systems.tar.gz and run the rnase_dodec_vsites benchmark from https://ftp.gromacs.org/pub/benchmarks/
I notice that this benchmark directory was updated on 23-Sept-2020 but after downloading found that the rnase_dodec_vsites files were exactly the same as the rnase_bench_systems_old-allbonds.tar.gz files.
Running the step to create the .tpr file:
gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top
I get the following error:
WARNING 1 [file topol.top, line 20602]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
VSITE
If you haven’t made a spelling error, either use the macro you defined, or don’t define the macro
As indicated, there was no #ifdef VSITE block in the topol.top file or any of the GROMACS 2020 include .itp files in <install_directory>/share/gromacs/top/amber99sb.ff
#include “amber99sb.ff/forcefield.itp”
#include “amber99sb.ff/tip3p.itp”
#include “amber99sb.ff/ions.itp”
Can you tell me how to resolve this error and run the rnase_bench_vsite as intended?
Thanks, Jan Fredin