Dear Daniel,
Thank you again for your comments and your intelligently method. I hope that
I can use your method for pulling of my DNA model properly.
with kind regards,
Ali
On Thu, Apr 28, 2011 at 5:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
--
Ali
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 28 2011 - 07:30:05 PDT
