Re: [AMBER] Question about SMD using polymer

From: Carlos Simmerling <>
Date: Mon, 6 Jul 2020 11:05:08 -0400

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
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 <>

> 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
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Received on Mon Jul 06 2020 - 08:30:05 PDT
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