[gmx-users] Potential of mean force

[abdul wadood]

Dear gmx user

First of all I am very thankful to all of you in helping me in the running of normal simulation using gromacs.
Now, I want to calculate pmf for enzyme ligand complex. I search for correct direction but not found anywhere.
There is tutorial on the gromacs website but it is for peptide peptide complex. Now, I dont understand how to specify the reference group to pull the ligand. 
The complex structure is attached. 
Any kind of help in this regard will be highly appreciated.

Many regards

Abdul Wadood, 
Research Scholar, 
Dr.Panjwani Center for Molecular Medicine and 
Drug Research, 
International Center for Chemical and 
Biological Science, 
University of Karachi, Karachi-75720, Pakistan. 
Email:wadoodbiochemist at hotmail.com 


 		 	   		  
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