More parameters fro gromacs-LIE simulations

[felipeZ]

Currently, the gromit script accept as input the protein and ligand coordinates and topology, together with the simulation time and the force-field. It would be nice if it can also accept the following parameters:

Parameter	Description	Type	Default
-vsite	Use virtual sites	bool	False
-solvent	Solvent model	str	Infer from force field
-elec	Treatment of electrostatic interactions (RF or PME)	str	Infer from force field
-t	Temperature	float	[200, 300] (K)
-tau	Coupling time for temperature	float	0.1 (ps)
-p	Pressure	float	1 (bar)
-ptau	Coupling time for pressure	float	0.5 (ps)
-d	Minimal distance between periodic images	float	2.25 (nm)
-prfc	Position restraint force constant	float	[200, 200] (kJ/mol/nm^2)
-at	Output resolution	float	0.002 (ns)
-rtc	Use roto-translational constraints	bool	False
-ndlp	Perform simulations in a optimal (NDLP) simulation cell	bool	False
-lie	Calculate ligand interaction energy	bool	False

Note: gromit predecesors accept a list of values for some parameters, for example:

./gmx45md.sh -f protein.pdb -name test  -l ligand.pdb,ligand.itp  -ff amber99SB -lie -d 1.8 -t 100,200,300 -prfc 10000,5000,50,0 -ttau 0.1 -conc 0 -solvent tip3p -ptau 0.5 -time 0.001 -vsite

[LourensVeen]

NDLP is not in the standard Gromacs, we should probably contact Tsjerk about this, and see if we can get it submitted to Gromacs somehow. Alternatively, we'd have to get a patched version from him, but I'd rather not have to maintain that...

It seems that -t is actually an array of floats. CWL supports arrays, but cwltiny doesn't at present. I'll have a look at whether to add that or to just make it a string for now.

Does -lie give additional outputs that we have to return?