Dear Amber developers,
I have a suggestion for a small update in the Amber manual regarding
constant pH simulations in explicit solvent.
For input preparation, the manual only states in section 26.2 to load
leaprc.constph in the tleap input.
However, a clear hint to also include the leaprc.water.tip3p file (or
similar) for explicit solvent simulations would be helpful, as is given
in the input example of Tutoral 33
(
https://ambermd.org/tutorials/advanced/tutorial33/Section1.php) by
Vinícius Cruzeiro.
In the tutorial's sample input, ion parameters are explicitely loaded
(frcmod.ionsjc_tip3p); this is not necessary (nowadays), because
leaprc.water.tip3p already includes that.
I know that the manual explicitely states that solvent models are to be
loaded separately (chapter 3), but it might be really helpful to repeat
this information for the constant pH simulation setup (chapter 26) and
provide a sample tleap input.
All the best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
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Received on Fri Jul 12 2024 - 02:00:02 PDT
