[gmx-users] How to construct PMF from the result of AFM pulling?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 7 16:31:56 CET 2006

clark wrote:
> Dear all:
> I have some problems about how to construct PMF(Potential of Mean Force) 
> from the result of AFM pulling function in Gromacs.After the "pull.pdo" 
> file was obtained and the force was calculated using the scripts writen 
> by Prof. , How can I get the PMF from the result(coordinate and force)?
> In theory, Should I have to perform several AFM pulling simulation from 
> different start points(conformation and velocity)??
> Thanks!I will appreciate it if some one would help me solve this problem?

How about reading some papers where they describe such simulations and


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