Dear all,
I was trying to pull a ligand from a protein using AFM pulling option of
Gromacs 3.3 but seems to be that it does not care about parameters that I
specify in pull.ppa file. In particular, in spite of the fact that I may
write to the input file coordinates of the unit vector describing the
direction of pulling, gromacs does it in its own way in the direction of axis
connecting centers of mass of reference and pulled groups AND not in the
direction indicated in *.ppa file. I tried also do not indicate the
reference group, thinking that it may work if pulling will be in absolute
coordinates but I failed again because program just connected center of
mass of the pulled group and point with coordinates (0 0 0)..
Does someone know how to make it working?
Thanks,
Kamil
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