Description

added a tutorial for multicomponent (multicomponent_tutorial.rst)

Updates

• added command input for MixtureBuilder()
• added files for the tutorial of generating a mixed solvent box (naphthalene in acetonitrile/water)

What to do next

all todos are included in the 'Note for AutoSolvate Developers' sections in the multicomponent_tutorial.rst file

• Please make command input for MulticomponentSolventBoxBuilder() class and MulticomponentParamsBuilder() class.

• test if the download link in .rst file works properly

• Please test if '-m' and '-s' command fully support both xyz and pdb file inputs which means if someone provides xyz file, the Multicomponent module will convert the xyz file into pdb file using openbable.

• Please implement a way to allow user to specify the solute charges and multiplicities.

   The idea case is allow user to provide a .inp document for the Multicomponent to read.
  
   For example autosolvate boxgen_multicomponent -m naphthalene_neutral.xyz -s solvents.inp
  
   The solvents.inp file will look like this:
      #xyzfile, charge, multiplicities
      water.xyz 0 1
      acetonitrile.xyz 0 1
  

• Please implement a way to allow user to use TIP3P water and other solvents AMBER already has force field parameters for.

• There are many flags in startmulticomponent() not working.

  -o, --output. Currently, we can not specify the output names. Please implement this feature and make sure it works.
  
  -r, --srunuse. Not implemented at all
  
  -e, --gaussianexe. Not sure if we need this flag.
  
  -d, --gaussiandir. Not sure if we need this flag.
  
  -a, --amberhome. Not sure if we need this flag
  
  -l, --solventoff. MixtureBuilder() can read solvent.off file, I have not implmented and tested this flag
  
  -p, --solventfrcmod Same as above.
  
  -g --chargefitting. Currently only support bcc. Please implement RESP charge fitting method.
  

• It seems the autosolvate mdrun command will not work if you use nohup. Please test and try to fix this issue.