Dear mohsen:
In US, there is no need to apply the force based on the COM. You can
select any reaction coordinate that you want. Be sure that the
reaction coordinate is not changing over time though (the COM is
particularly refractory to this, which is probably why it is used, in
addition to the COM being conceptually simple). The good news is that
you check this like you check every convergence issue is US -- by
block averaging your data and ensuring that there is no drift over time.
Note though that US is not the only method to get binding free
energies and you might want to try free energy perturbation with the
gromacs "free energy" code instead of using the gromacs "pull code" to
do US.
Chris.
-- original message --
Dear All
I want to pull my ligand from protein which is docked to it for generating
configurations for umbrella sampling.
But my ligand is located in a hole inside of protein.
If I pull it along the line which is connecting COMs of them,the ligand may
be arrested(constraint)inside of hole.
Am I force to pull ligand along this line or I can pull along any line for
generating configurations for umbrella sampling?
I think the important is to pull it out from the binding pocket and we need
to pull it along a line
which is connecting the center of pocket(no protein's COM)to ligand's COM.
What do you think.
Thanks in advance
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