sorry I don't have any good suggestions for how to do that along a
particular direction - it seems to me that the second chain will
probably move quite a bit and you might need internal coordinate restraints
(dihedrals) if you want to keep it fairly rigid and pull to see the shear
motion. others on the list might have experience with using restraints to
pull in a certain direction - perhaps the collective variables in the NFE
module would be helpful
https://ambermd.org/tutorials/advanced/tutorial31/index.html
On Fri, Jul 10, 2020 at 4:25 PM Pinky Mazumder <pmazumder67.gmail.com>
wrote:
> Hi Carlos,
>
> Thank you so much for your response.
>
> Attached is the picture of my two cellulose chains. I want to fix ( will
> not move ) the bottom chain.
>
> I also want to pull the top chain so that the (O,H bond can break or
> reform) and I can see the shear.
>
>
> I think your second option will be applicable for me. Isn't it? If it will
> work, then please let me know how to perform this type of SMD simulation.
> Or what should I follow?
>
>
> Thank you again.
>
>
> Sincerely,
> Pinky
>
> On Mon, Jul 6, 2020 at 10:05 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > it depends on what you mean by "fixed". if you mean moving but generally
> > staying in place, cartesian restraints can work (also depends on
> > which atoms are "fixed"). If you mean not moving at all, that's a bit
> more
> > difficult.
> > since the zero in space is arbitrary, another option is to move one chain
> > relative to the other using distance or other internal coordinate
> > restraints. again it depends on what you mean by fixed.
> >
> >
> > On Mon, Jul 6, 2020 at 11:02 AM Pinky Mazumder <pmazumder67.gmail.com>
> > wrote:
> >
> > > Hi all,
> > >
> > >
> > > I want to observe the shear between the two polymer chains
> > > (*carbohydrates*).
> > > Together, my both chains have 216 atoms. I placed them 8 Angstrom apart
> > > from each other.
> > >
> > >
> > > Now, if I want to pull one chain having another one fixed, what should
> I
> > > do?
> > > Do I Need to modify the Distance Restraint File of *ASMD Tutorial 26
> *of
> > > AMBER? Am I on the right track? If not please shed some light on my
> issue
> > > or recommend me any other tutorial.
> > >
> > >
> > > Thank you.
> > >
> > > Sincerely,
> > > Pinky
> > > --
> > > Pinky, Sharmi
> > > AL,US
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> > >
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> >
>
>
> --
> Pinky, Sharmi
> AL,US
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Received on Mon Jul 13 2020 - 07:30:04 PDT
