Brief description of tools/files: PTM with GROMOS
Link: http://vienna-ptm.univie.ac.at/
I am trying to run a simulation with methylated residues. I have tried applying a GROMOS forcefield as according to the Vienna PTM procedure but ran into :
WARNING 1 [file topol.top, line 14360]:
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 .
since i have been trying to find a way to manually edit other forcefields as to accomidate my structure ( Adding a Residue to a Force Field). Are there any additional resources or examples that can help me as i develop a system with checks to validate my addition?