GROMACS modification: No
I’ve ran several simulations with mixtures of methyl-THF (forcefield & parameters from charmm36) and water. For some reason, when running gmx rdf with following command line, I get weird artifacts in the beginning of RDF graphs. I checked the boxes and they haven’t phase separated.
gmx_mpi rdf -f md-297.xtc -s md-297.tpr -o thfm-thfm_rdf.xvg -ref THFM -sel THFM
Box size is 200 molecules.
Could this be something to do with the simulation settings or box size?