On Sat, May 12, 2012, ros wrote:
>
> Your RST file would be something like this:
>
> ### Restraints par 1-34
> &rst
> iat=1,34,
> r1=27,
> r2=27.5,
> r3=27.5,
> r4=28,
> rk2=5.0,
> rk3=5.0,
> /
A few comments:
1. The above file will add a restraint between _atoms_ 1 and 34, not residues
1 and 34.
2. For umbrella sampling, you very probably want a harmonic restraint, so
that you can remove easily it in later analysis. If so, you need to have
r1 << r2 and r4 >> r3, so the system will not leave the harmonic portion
of the restraint space.
3. The original question was a little ambiguous:
> > I need to exert external force between two residue to these two
> > residue separate from each other....
> > I will use umbrella sampling. but I don't know how write dist.RST file?
The use of umbrella sampling is what the above distance restraint could do;
different windows would have varying values of r2=r3. This external (biasing)
potential is rather different that "applying an external force".
....dac
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Received on Sat May 12 2012 - 11:00:03 PDT
