Calibration of correction potential in constant pH GROMACS

User discussions
1

GROMACS version:
GROMACS modification: Yes (constant pH)

Hi,

I am looking at using the constant pH implementation of GROMACS by Aho et al. 2022. Looking through their tutorials there is one for calibrating the correction potential implemented in this fork. Is the calibration necessary? I am using the phbuilder tool and in the generated mdp files, I already have the polynomial fit. Can someone please help?

Thanks!

2

Hi,

Which molecule are you interested in simulating with the cpHMD method? The standard amino acids (LYS, ARG, GLU, ASP, HIS) are already parameterized for the current cpHMD implementation in GROMACS and require no further calibration. If you wish to simulate a novel residue (e.g., a small molecule), you will likely need to generate new correction-potential coefficients.

Best regards,
Marius

3

Hi Marius,

Thanks for the quick reply! I do not have any non-standard residues in the transporter I am simulating so that resolves my question. Thanks! :)