[gmx-users] PMF from AFM pulling

[bmmothan at ucalgary.ca]

Dear gromacs users,

I would like to obtain a potential of mean force (PMF) plot from an AFM
Pulling calculation.

I used AFM method in the Pull code to separate two strands of peptides
along their center of mass reaction coordinate.

here is the parameters I used:
runtype = afm
ngroups = 1
reference_group = receptor
group_1 = ligand
reftype = com
pulldim = Y Y Y
afm_rate1= 0.0004
afm_k1 = 10000
afm_dir1 = 0.2284214  -0.940737 -0.24730
afm_init1 = 0.17445  -0.71846 -0.188685

As you can see, I pulled in all dimensions, and my pdo file contains all
three coordinates.

I have searched the list but didnt find away to analyze the data to obtain
a free energy profile. any help will be appreciated.


Belquis