[gmx-users] afm pulling

Marta Murcia mam2070 at med.cornell.edu
Wed Apr 26 17:36:15 CEST 2006

Dear all,
I am simulating an unbinding process with the pull code (afm option).
I've been reading previous posts about this option and I just wanted to 
clarify some ideas and ask some questions. There are:
1-The pulling can be done choosing two different molecules. Why a 
particular group within a molecule can not be used? Not even as a 
reference group?
2-Should I need to fixed the center of mass of the protein to avoid 
shifts? How can I do that? Would it be OK to use posre for the backbone 
of the protein with carrying out the pulling?
3-Should I removed all the constraints for the bonds (SHAKE, lincs)?
4-once I have the pull.pdo the calculation of the applied force will be 
F= K*(zspring -zgroup) (assuming I am pulling in the z direction)?

Thanks in advance for your help. Appreciated!

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