Re: [AMBER] Question about SMD using polymer

From: Pinky Mazumder <pmazumder67.gmail.com>
Date: Fri, 10 Jul 2020 15:24:35 -0500

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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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>


-- 
Pinky, Sharmi
AL,US



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Received on Fri Jul 10 2020 - 13:30:03 PDT
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