GROMACS version: 2023
GROMACS modification: No
Hi all,
I want to perform an MD of a small symmetric metal neutral complex (contains transition metal atoms with coordinated carboxylate groups and acetonitrile). There is an X-ray structure I can start from (cif). As many before me, I have trouble generating the topology file for Gromacs. I have tried the acpype server, the charmm-gui-server, the atb-server but each give me errors. I suspect that the problem is either the heavy metal, the coordinative bonds, the delocalised bonds and/or the charge distribution.
But maybe I am overcomplicating my problem. I am only interested in a rough estimate of the rotational correlation time of my relative rigid complex and its anisotropy along the symmetry axes. Perhaps Gromacs is not the right tool (I have very little MD experience and the little I have is with gromacs (8 years ago!)). Any suggestion?
best
CF