I have two different sets of atoms one including bonds and angles with SHAKE
but the other atoms do not have bonds and I cant apply minimization to these
nonbonded atoms because minimization is not used with SHAKE. I read the doc
and the mail list, also ‘fix shake % energy minimizations ‘ post, but I
couldnt find the exact answer. Can I apply minimization to a specific group
you *can* minimize such a system, all you need to do is to temporarily
increase the force constants for bonds and angles that are constrained
with SHAKE, say by a factor of 100 or so. that is a very good
approximation and unlike MD, minimization uses adaptive steps, so
having a steep potential is not that much of a problem.
of atoms(ones without SHAKE) just to make them not to move far away on the
equilibration. This explosion happens only for nonbonded atoms, it is OK
with the ones with SHAKE.
this is also possible, you can just temporarily replace fix shake with
fix setforce 0.0 0.0 0.0 and the atoms that you want to "shake" should
not move at all during minimization.