[gmx-users] questions about umbrella sampling tutorial

Albert mailmd2011 at gmail.com
Fri Apr 5 09:29:33 CEST 2013


  I am trying to do umbrella sampling for a protein/ligand water system 
these days following Justin's nice tutorial. And I've got some questions:

(1) in the tutorial, the small peptide was pulling along Z direction. I 
am just wondering, will the small peptide be pulled in both +Z and -Z 

In my case I've got a ligand in the deep pocket, it is possible that the 
ligand can escape the binding pocket from two opposite site, let's say 
-Z and +Z which I hope the umbrella sampling can give me some evidences 
to prove this....  Could the umbrella sampling answer this question? Or 
we should pull the ligand along X,Y and Z three direction so that it is 
more convinced?

(2) it is said that when doing free energy calculation in gromacs, we'db 
better use double precision Gromacs. So probably we have to use CPU 
instead of GPU for this?

thank you very much

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