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MobleyLab / relative-solvation-paper

Paper on reproducibility of relative solvation free energies across packages
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Reviewer 2-Q17: GROMACS water constraints #57

Closed Steboss closed 6 years ago

Steboss commented 6 years ago

Why was not SHAKE used for waters with Gromacs.

davidlmobley commented 6 years ago

I think it was, or at least, waters were constrained (probably with LINCS which is the GROMACS default). @gduarter please check.

Do you know why the reviewer has this impression, @Steboss ?

Steboss commented 6 years ago

This could be also a clarification needed in SOMD.

Basically, both AMBER and CHARMM paragraphs ( in RAFE setup section) we have explicitly written " water hydrogens (TIP3P) were constrained with SHAKE". However, this is not said neither in GROMACS nor in SOMD paragraphs. This could lead to some confusion, so I think it's better to add a similar statement.

davidlmobley commented 6 years ago

OK, so this is a minor clarification for all cases I think.

jmichel80 commented 6 years ago

For Gromacs wrote: No holonomic bond or angle constraints for the solutes were used. Waters were constrained with LINCS. @gduarter please correct if this is wrong.

gduarter commented 6 years ago

@jmichel80 - yes, your statement is correct.