[gmx-users] questions about umbrella sampling

[mircial at sjtu.edu.cn]

Dear All:

I am using umbrella sampling method to calculate potential of mean  
force and I encountered the following questions:
1, at the *.ppa file, I need to incorporate a parameter indicating the  
"the position of the pull group will restraint to, relative to the  
reference group" (i.e., the "pos1" parameter).

To my understanding, in the initial structure, the pull group is not  
need to at the exact position defined by the aformationed parameter  
("pos1" parameter) in the .ppa file. I just need to put the pull group  
near that position, am I right?

2, Since I need to define the position of the pull group relative to  
the reference group. I need to calculate the mass center of the  
reference group as well as that of the pull group. Does there any  
tools in GROMACS to calculate their mass center?

Thank you very much for your time and your kindness!

Best Regards

R-X Gu