fixing parts of an equilibrated protein's environment

From: Sebastian Stolzenberg (
Date: Wed Sep 09 2009 - 10:26:17 CDT

Dear All,

I have an equilibrated protein embedded into a membrane, and I would
like to fix some major parts of the system.

Do any NAMD protocols exist that can handle do? What is the best
strategy in general?

I tried increasing constraints, prior minimizations, decreasing in the
Langevin Damping, ....
I always end up with RATTLE constraints or too high velocities or
particular atoms.
Shall I try "freezing" the whole system, by decreasing the temperature,
and then increase it again for only the parts I want to keep flexible?

Thanks a lot,

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