GROMACS version: 2022 GROMACS modification: No Dear All, I am trying to get the energy minimized structure of a 10x10 Platinum surface with 3 layers along with a single ion pair ionic liquid (1-butyl-3-methylimidazolium tetraflouroborate). During the energy minimization, it shows some LINCS warning, printing the atoms and bonds that rotated more than 30 degrees, and the potenti…

GROMACS version: GROMACS modification: Yes/No Hi everyone, I am beginners in GROMACS and I am trying one tutorial on youtube by Molecular Dynamics Tutorial | Protein-Ligand Complex: GROMACS - PART 1 - YouTube. However, there were some errors as shown below: Fatal error: atom C1 not found in buiding block 1MET while combining tdb and rtp May I know how to solve this because in…

Dear community, I have a question that bothers me for a long time. Is there are MD-specific repositories, that automatically generate metadata and might be considered as good for FAIR sharing? (For now Zenodo and NOMAD are considered, but first is general purpose and second seems to be concentrating on QM data). If there are no such repositories, what would be a minimal set of da…

GROMACS version: 2022.3 GROMACS modification: No Hi everyone, I am using CHARMM-GUI for the preparation of a protein which has copper ions inside its structure but I’m having some problems keeping them in their position during the simulation. In gromacs I usually introduce harmonic restraints but I don’t know how to do it within the topology file I obtain from CHARMM-GUI. For av…

GROMACS version: 2022 GROMACS modification: No Hi all, I’m trying to install gromacs-2022 (2022.3 didn’t work, waited for 2022.4 and got the same problem) but “make” fails with the following error: [ 92%] Linking CXX shared library ../../lib/libgromacs_mpi.so /home/user/Downloads/gromacs-2022.4/src/gromacs/mdlib/lincs.cpp:90:8: warning: type ‘struct AtomPair’ violates the C++ On…