GROMACS version: 2021.5
GROMACS modification: Yes (PLUMED 2.7.3)
I’m trying to set up REST2 simulations for a protein in a box of water. I have done the following so far:
1- Briefly relaxed the solute in a box of water (regular NVT simulation).
2- Ran gmx grompp on the topology file.
3- Produced scaled topology files with plumed partial_tempering.
When running grompp on the processed topology files, I get the following warning (except for the first, unscaled, topology file):
NOTE 2 [file sys_scaled_1.top, line 236689]:
System has non-zero total charge: -0.139728
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
WARNING 1 [file sys_scaled_1.top, line 236689]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
Given that the PLUMED website says partial_tempering doesn’t work with CHARMM CMAP, am I trying to set up a system that won’t work? I’m not sure if the error is even related to this statement. I have seen papers in literature that use the CHARMM36 force field along with REST2. What am I missing?