[AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation

From: Pinky Mazumder <pmazumder67.gmail.com>
Date: Fri, 8 Jan 2021 19:11:43 -0600

Hi all,

For steered molecular dynamics simulation, in the tutorial-26, it is showed
that how to pull one helical peptide chain. But, if I have one layer
consists of several chains, then how to pull that layer?

What would be the value in (iat=?, and how to assign the distance r2=?)

Please guide me if you have any idea?


dist.example.RST
<https://ambermd.org/tutorials/advanced/tutorial26/files/dist.example.RST>

 &rst
        iat=9,99,
        r2=13,
        r2a=17,
        rk2=7.2,

 &end




Thank you.

Sincerely,
Sharmi 
-- 
Pinky, Sharmi
AL,US
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Received on Fri Jan 08 2021 - 17:30:02 PST
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