Zhiyi Wu

@lohedges Thank you. I have used `antechamber -i lig.pdb -fi pdb -o ligand.sybyl.mol2 -fo mol2 -c bcc -s 2 -at sybyl` to generate the mol2 file as input, but it...

This is how I usually create the openFF format from mol2 file if it could be helpful. ``` try: from openmm.app import PDBFile except ImportError: from simtk.openmm.app import PDBFile import...

@lohedges Thank you for the reply. I wonder if there is a plan of adding one? As for gromacs, one might wish to have the flag `-update gpu` to use...

@lohedges Thanks for the comment. I wonder if it is possible to have an interface similar to ``` freenrg = BSS.FreeEnergy.Relative(system, protocol, engine='GROMACS', ) freenrg.setArg({"-ntmpi": 1}) ``` Where the Arg...

@lohedges Thank you for the explanation.

@lohedges Thanks. Do you need to review it? In the last time when I try to merge some functionality, you have given some valuable advices? https://github.com/michellab/BioSimSpace/pull/328

@lohedges Thanks for the help. Is solving the conflict very difficult? I think the best route will be create a branch from Exscientia:devel to be Exscientia:michellab, then merge michellab:devel to...

Waiting for https://github.com/michellab/Sire/issues/407 to be fixed.

I have merged the dev to our dev. I wonder if you mind review this PR when you are free, please? Thank you.

I haven't used SOMD but I guess if we have this as pandas.DataFrame all these ``` "discharge_soft" : Perturb all discharging soft atom charge terms (i.e. value->0.0). "vanish_soft" : Perturb...