SMD on a group of atoms: Confusion

From: Vani Krishna (
Date: Wed Sep 01 2004 - 10:47:41 CDT

Hello all:

Thanks for all the previous replies regarding patches
on protonation .

I have a question regarding doing SMD simulations on a
group of atoms. From the User guide, i understand that
when i want to 'pull' a group of atoms, i can specify
the group by changing occupancy column. What iam
confused about is that how the center of mass of the
protein is held fixed? Iam trying to pull a molecule
from inside of the protein into solution and when i do
this, the whole system moves, which is obvious as I
have not fixed the protein COM. Iam new to SMD and any
suggestions/references in this regard would be most

Is there a way to perform multiple SMD at the same
time? i.e, pull group A in {x1,y1,z1} and group B in


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