Good afternoon,
I'm currently working on simulating an organic ligand transport across a lipid membrane to investigate the potential of mean force (PMF) along the translocation pathway. For this setup, I have decided to start the ligand at the center of the membrane (z=0) and move it outward to the extracellular site, aiming to expedite energy convergence. The membrane center is set as the origin (0 kcal/mol), with methanol moving away from this center.
However, when analyzing the trajectory, I observed that the PMF values increase as the molecule moves outward. Ideally, the PMF profile should decrease with increasing distance, reflecting the expected energetic favorability as it exits the membrane center.
The trajectory visualizations in VMD confirm that methanol is moving as expected, suggesting that the issue may stem from the energy calculations or PMF setup rather than the actual pathway. I've double-checked my initial configurations, energy file outputs, and calculation intervals but haven’t identified the root cause yet.
I’d appreciate any advice or insights from others who have encountered similar issues in PMF calculations within membrane simulations. I have been following the online tutorial AMBER-Umbrella_COM_restraint_tutorial<
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial>
(
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial)
[
https://opengraph.githubassets.com/a54a5c523052ed44e7b360e86603aba0f4feefc5a0783e2d9cb66bfe607bcff9/callumjd/AMBER-Umbrella_COM_restraint_tutorial]<
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial>
GitHub - callumjd/AMBER-Umbrella_COM_restraint_tutorial: Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane<https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial>
Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane - callumjd/AMBER-Umbrella_COM_restraint_tutorial
github.com
Thank you!
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Received on Mon Nov 04 2024 - 16:00:02 PST
