GROMACS version: 2025.1
GROMACS modification: No
Hi, I’m trying to calculate the dimerization free energy of a hydrophobic molecule that contains a small graphene nanosheet and several side chains. I used the WTM-eABF method of the colvars module.
Two CVs were adopted: 1, the distance between COMs of the two molecules; 2, the torsion angle between the two molecules.
I tried several different MtD parameters (hillwidth, hillweight, biastemperature) and I also tried to use the eABF method solely, however, the simulations always got crashed after several tens of nanoseconds. Sometimes I got the segmentation fault error, and at other times it’s cuda error#700. The mdp and colvars configuration files were attached below.
I don’t know what other settings I can still modify now. I would appreciate any suggestions. Thanks a lot.
mdNPT.mdp (1.9 KB)
colvars.txt (1.7 KB)