AMBER Archive (2005)

Subject: AMBER: potential of mean force calculation along reaction coordinates

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jul 26 2005 - 02:04:00 CDT

Dear Amber users£¬

I am trying to calculate the potential of mean force along reaction coordinates of proton transfer in explicit solvent. The reaction can be represented as O1---H---O2 for simplicity. The simplest one, i.e. 1D reaction coordinate, is defined as the difference between R(O1--H) and R(O2--H). Since the solute is very small, there is no cut of covalent bond and the whole solute is treated quantum mechanically. For accurate PMF, umbrella samplings are needed along the reaction coordinate, and biasing potentials centered at some predefined grids are needed to bias the sampling.
I have some questions about how to implement it.
1.how to fix the distance between O1 and O2? And how to define the difference between R(O1--H) and R(O2--H) and apply the biasing potentials to the QM zone?
2.how to define a series of biasing potentials at different grids along the reaction coordinate in a series of MD simulations respectively?
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Best regards,

Ye Mei
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-07-26

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