GROMACS version:2019.04
GROMACS modification: No
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Dear Gromacs users,
For a protein(ion channel here)-membrane system, I would like to know the 3D distribution of the potential in the protein pore (at a specific time) for further analysis. Is there any way to get this from the simulation results? I know calculating the potential distribution in the system is a must-step for gromacs. But how to get this intermediate data? Many thanks for your help.
Hopefully I don’t need to calculate myself based on the Interaction function and force fields.
I don’t believe that Gromacs has a way to output this at the moment, but maybe it has been added.
Do you require the full potential, or is the electrostatic part sufficient? For the full potential, I am not sure what the best method is. For the latter, you can read your configuration into VMD and use its PMEPot plugin to calculate the 3D potential, instantaneous or averaged over some frames. The charges can be supplied by creating a .psf file for you configuration (just ensure that the total charge is 0 – if Gromacs writes the .psf file, the charge values can be truncated and not cancel perfectly).
This is of course assuming that you ran with PME electrostatics.
Super thanks. I was actually thinking about the full potential, which better includes the vdw, the non-bonded and bonded interactions ect, like what GROMACS considers. But it is pretty good to know a way to calculated the electrostatic potential. Thanks again.