Hi,
Constant force pulling can be approximated using a distance restraint
(with nmropt=1). This is possible because restraints in amber are by
default a well with a square bottom with parabolic sides out to a
defined distance, and then linear sides beyond that, like:
linear < r1 < parabolic < r2 < square < r3 < parabolic < r4 < linear
The restraint force is constant in the linear regions, so if you set
the atoms of your restraint to the two endpoints of your pull, and set
r1-r4 to be around the final distance you want, there will be a
constant force acting to pull the endpoints to that final distance.
rk2 and rk3 control the strength of the force. Here is an example
disang file for pulling between atoms 3 and 992 to a final distance
around 208 Ang.:
#
# distance restraint constantF
&rst iat=3,992,0
r1 =206.22, r2 =208.22, r3 =208.22, r4 =210.22, rk2 =0.25, rk3 =0.25,
nstep1=0, nstep2=0,
&end
&wt
TYPE="END",
&end
DISANG=pull.disang
See the users manual for more details (section 6.1:Distance, angle,
and torsional restraints in particular).
-Dan
On Thu, Apr 28, 2011 at 8:55 AM, Ali M. Naserian-Nik
<naseriannik.gmail.com> wrote:
> Hi all,
>
>
> I know that currently SMD simulations at constant force are not directly
> possible in AMBER. Dr. Roitberg, in one of his emails to the Mail Reflector,
> has explained very briefly a method for pulling with constant force. Here is
> his explanation: “You can have a moving center if you want to apply a
> constant velocity pull, or user the ends of the flatwell restraint to fake
> constant force pullings (Thanks to Dan Roe for this last insight!).” Could
> you please help to clear the method that has been suggested by Dr. Roitberg
> or other suitable methods, in details, for constant force pulling?
>
> Thank you very much,
>
> Ali
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 28 2011 - 07:00:07 PDT
