Brief description of tools/files: Tools used for this are GROMACS 2023.4 (Installation guide - GROMACS 2023.4 documentation), Martinize (martinize), and Insane (GitHub - Tsjerk/Insane: INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems).
Tools are being used as GROMACS to run simulations, Martinize to coarse grain atomistic proteins, and Insane to insert coarse grained protein into coarse grained lipid bilayer+hydrate system.
Contact person (name and email address): Zachary Miller @ zamydm@iastate.edu
How the work has been tested/reviewed: Work has been conducted on Mac M2 operating system. All necessary packages have been installed and configured properly. No issues outside of below issue has been noted.
Good Morrow.
I am admittedly new to running simulations in GROMACS having only ran a few trial simulations, and I was wondering if anyone has experience with running simulations on coarse grained systems generated by Martinize+Insane? I for the life of me have been unable to get these simulations working, and the error outputs of GROMACS have not been particularly helpful. I am currently at the energy minimization step, though advice for NVT/NPT stabilization are also appreciated. Command line and error below:
Command line: gmx grompp -p 8HKQCoarseLipid.top -f min.mdp -c 8HKQCoarseComplete.gro -maxwarn 10
Error: zsh: abort gmx grompp -p 8HKQCoarseLipid.top -f min.mdp -c 8HKQCoarseComplete.gro 10
I was just rather naively hoping that someone has experience with setting up and running simulations of these systems and if you could give advice on how you conducted your simulations. Thanks so much!