From: Ryan McGreevy (
Date: Wed Mar 26 2014 - 11:25:55 CDT

You can run mdff on multiple structures the same way you would run them in
a standard NAMD simulation. You just need a pdb and psf of your system
(and all the corresponding standard mdff files) and run mdff normally.
 Sometimes it is useful to fix certain structures and delete their
corresponding density while you fit another part of the system, but this is
dependent on your particular system.

On Tue, Mar 25, 2014 at 8:59 PM, Lyman K Monroe <> wrote:

> I am interested in mdff to fit multiple pdb structures to a single map
> simultaneously.
> Is there a way to run these structures simultaneously so that they will
> sterically interact and prevent one another from being pulled across the
> map?