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!
Best
M
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