Re: [GaMD-discuss] Utilization of 3D-PMF

[Yinglong M. <yin...@gm...>]

Hi Chanyann,

Yes, the way 3D-PMF works for ligand binding can be similar for protein-protein interactions (protein binding). You just need to find the proper reactions coordinates from watching your simulation movies. Reweighting is generally recommended to get the “real” energy minima.

Best,
Yinglong


Yinglong Miao, Ph.D.
Associate Professor
Computational Medicine Program and
Department of Pharmacology
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

> On Dec 25, 2023, at 9:23 PM, cha...@st... wrote:
> 
> Hello,
>    I am using GaMD to study the interaction of a protein-protein complex, and I noticed that the 3D-PMF are available now for lig-gamd and pep-gamd. I wonder that if I can select three reaction coordinates (such as RMSD of protein A, RMSd of protein B and the distance between protein A and B) and using noweight method to find the energy minima?
> Best wishes,
> Chanyann
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