gmx solvate only updates topology when the solvent is "SOL" - Redmine #1929
Archive from user: Chris Neale
“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:
echo 3 3 3
gmx solvate -cp empty.gro -cs spc216.gro -p empty.top -o out.gro
- 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.
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.
(from redmine: issue id 1929, created on 2016-03-25 by gmxdefault, closed on 2018-08-13)
- Revision 9931becc by Kevin Boyd on 2018-08-06T12:21:02Z:
Fix gmx solvate topology updating The topology update of gmx solvate was hardcoded to SOL molecules (and some of the reported quantities also registered HOH and WAT). Changed to allow updates based on any solvent molecule information. Also, now allows for updates with multiple solvent molecule types in the input solvent configuration Added test case for topology update with multiple solvents fixes #1929 Change-Id: If506e0f509c8a25cb615fb8d3f15b4dfdb239afa