Hello everyone:
I prepar to make a QM/MM simulation by employing gromacs compiled
with mopac, and need to define two groups which are treated by QM and MM
separately, the question is this: during the dynamics course of my research
system, particles will enter/leave the QM zone, so there is a
changing-particle-number situation in the QM zone, I checked the information
about command "make_ndx", which seems define a group by atom type, name, or
residue and so on, but in my situation I need to define a group by space,
namely define all atoms have a distance from a fixed coordinate shorter than
a given radii as a QM group while the rest atoms are defined as MM group
(the group members will change during the dynamic course), but I don't know
whether "make_ndx" can achieve this purpose? If can not, is there any other
methods can define groups by space?
Forgive my unfamiliar English and thank you, I appreciate for your
reply.
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