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Feature #2036

gmx solvate should work with molecules

Added by David van der Spoel about 3 years ago. Updated about 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Difficulty:
simple
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Description

gmx solvate can not handle molecules as solvent. According to the documentation it uses the residue number in the input file, ("In practice
this means that two subsequent solvent molecules in the solvent coordinate
file should have different residue number.") but this is not entirely correct since the residue names are interpreted as well. As a results a molecule containing more than one residue with different names (even if they have the same residue number) is torn apart by gmx solvate.

The obvious solution would be to use real the molecule information in a tpr file.

History

#1 Updated by Teemu Murtola about 3 years ago

It interprets residues exactly like every other Gromacs program, but the help text hasn't been updated to match the new implementation that also considers residue names.

A workflow that would require a tpr file as solvent would not be particularly practical, either.

#2 Updated by David van der Spoel about 3 years ago

I agree a tpr file is a hassle, however now it is impossible to dissolve a protein into a solution containing other molecules. In fact the code already reads tpr files and extracts topologies, so it will not be too hard to fix.

#3 Updated by Teemu Murtola about 3 years ago

Note that is we want to really use gmx_mtop_t everywhere, the whole tool and the helpers it uses needs to be rewritten to not use t_atoms, and that will also probably solve this. Doing something else is likely to waste significant effort (since you would need to make the helpers aware of molecules, in a way that is not compatible with gmx_mtop_t).

#4 Updated by Teemu Murtola about 3 years ago

I would also argue that the behavior that would fit into a typical workflow would be that the tool would read the molecule types from the .top file given as input (if present) and recognize those from the structure file.

#5 Updated by David van der Spoel about 3 years ago

In fact gmx insert-molecules can work as stand-in for the desired functionality, it can even insert whole proteins. So no need for this feature.

#6 Updated by David van der Spoel about 3 years ago

  • Status changed from New to Closed

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