GROMACS

"gmx solvate -p" only updates topology when the solvent is "SOL". It would be nice to add this feature for other solvents as well.

For example, compare that it works for SOL:

touch empty.mdp {
echo title
echo 0
echo 3 3 3
} > empty.gro
gmx solvate -cp empty.gro -cs spc216.gro -p empty.top -o out.gro

1. now empty.top lists the number of SOL added.

However, when I instead try:
gmx solvate -cp empty.gro -cs ./methanol5ns.gro -p empty.top -o out.gro

then the out.gro output is as expected but the lines are not added to the .top file as desired.

Note that the following output from gmx solvate indicates that the necessary information is already known by the program that the molecule is MEOH and 354 such residues were added.

Sorting configuration
Found 1 molecule type:
MEOH ( 6 atoms): 354 residues
Generated solvent containing 2124 atoms in 354 residues
Writing generated configuration to out.gro

Output configuration contains 2124 atoms in 354 residues
Volume : 27 (nm^3)
Density : 741.494 (g/l)
Number of SOL molecules: 0

I have included a charmm methanol .itp and .gro for reproduction, but you don't even need that. Just take share/gromacs/top/spc216.gro and change all "SOL" to some other name and again gmx solvate will fail to update the topology.