GROMACS version: 2021 and further
GROMACS modification: Don’t know
Hi Everyone,
I’m currently trying to use the constant pH tool of gromacs. As reported in the GitLab tutorial:
You can find a " start_param " script asking for the " md_cph " mdp file. In the latter, I was wondering whether all the keywords/parameters reported under the “CONSTANT PH” comment line really exist in the gromacs versions from 2021 on.
Indeed, I show you here the way constant pH functionality has been announced (if you go back up to the “gromacs-constantph” directory): it refers the reader to the article " Scalable Constant pH Molecular Dynamics in GROMACS , J. Chem. Theory Comput. 2022, 18, 10, 6148–6160", where you can find the words “We have implemented the algorithms for CpHMD with charge
interpolation in a fork of GROMACS software package (2021
release).” So has that fork been merged in the main developing branch, or is it still under revision? In other words, if I download 2021+ versions, am I able to run the tutorial and make gromacs understand the cited keywords/parameters?
In fact, I read this statement " 2. Download the gromacs-constantph beta build. " in the following repository of the so called “phbuilder” tool:
which has been recenlty developed for automating the creation of constant pH files. The “beta build” words give me serious doubts …
For example, up to now I noticed that the 2019.3 version doesn’t read the parameters under the “CONSTANT PH” I cited. If I install the 2023 version, will those keywords be readable?
A last question: from the article of the abovementioned “phbuilder” : “phbuilder: a tool for efficiently setting up constant pH molecular dynamics simulations in GROMACS , ChemRxiv, 11 August 2023”, I understood that for non-coarse grained simulations, the only FF currently at disposal for running CpHMD is the charmm36m one: am I right? Indeed, the DOI reports: “Currently, the GROMACS constant pH implementation only supports
a modified version of the charmm36m force field,” . I think this is a major limit of constant pH in gromacs with respect to competitors such as amber.
I kindly thank you for your interest, hope my issues will clarify the topic to others, too.
Best Regards,
Jacopo