Roy Haolin Du comments

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                                            Roy Haolin Du

Positional restraints error in runFreeNrg: property format mismatch between setupPositionalRestraints and atomNumVectorListToProperty

Hi Lester, Thanks a lot. But I currently only have these two files. I’ll ask Fred for the rest so we can fully reproduce the issue. Also, I’d like to...

Positional restraints error in runFreeNrg: property format mismatch between setupPositionalRestraints and atomNumVectorListToProperty

Hi Lester, Thanks so much for letting me know more about the position restraints, that’s really helpful! Actually, we do have one working case where `somd.cfg` uses: ``` cutoff type...

Positional restraints error in runFreeNrg: property format mismatch between setupPositionalRestraints and atomNumVectorListToProperty

Thanks so much for your kind help, I really appreciate it. I completely agree with you, especially considering the logic: ``` if cutoff_type.val == "PME": fep_cls = Sire.Move.OpenMMPMEFEP else: #...

Support Membrane Protein pre-equilibration in Biosimspace via Gromacs

Thanks! I was able to overwrite the `.mdp` parameters using `extra_options` method, and that worked very well！ However, I’m wondering is there a way to separate different groups? (as done...

Support Membrane Protein pre-equilibration in Biosimspace via Gromacs

Thanks Lester! And sorry for following up with one more question, please! For temperature coupling groups (protein/membrane/solvent separation) in `gmx.mdp` file, `tc-groups = SOLU MEMB SOLV`. I can create a...