[gmx-users] afm pulling
ewalton at MIT.EDU
Thu Apr 27 01:01:26 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?
Any group that is defined in your index file (specified with mdrun -
pn pull.ndx) can be used. Look at made_ndx in the manual to learn how
to add new groups.
> 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
> of the protein with carrying out the pulling?
It depends on what you want to do. Typically, something would need to
be fixed. In ligand-protein systems, the center of mass of the
protein is a reasonable choice. It was used by Grubmuller et al. in
their 1996 Science paper on the unbinding of biotin-streptavidin.
(Science, 271:954–5, 1996) For unraveling of proteins, one terminal
atom may be fixed while the other is pulled.
Fixing the center of mass of a group in the index file can be done in
the .mdp file you feed to grompp. See the manual, chapter 7.
> 3-Should I removed all the constraints for the bonds (SHAKE, lincs)?
I think this is a matter of preference. Some people do, some people
don't. Again, it will depend on your system- is it stable without the
The bonds that are broken with afm pulling are bonds described by non-
bonded interaction terms in gromacs. These bonds wouldn't be
constrained by shake or lincs anyway, so the presence or absence of
constrains should have a minimal effect on the simulation results.
> 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)?
Yes. The spring is an ideal spring, so force is k*(extension). The
extension can be calculated from the pull.pdo file.
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