Re: [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein

From: Chetna Tyagi <>
Date: Wed, 17 Apr 2019 09:57:18 +0200

Dear Mayank,

you can reweight any distribution that you want. It can be for every
dihedral angle distribution if you need or a phi-psi 2-dimensional
distribution in case of producing free energy landscapes.

In the example, they calculate phi-psi distribution for an alanine
dipeptide which is ACE-ALA-NME so will have one phi angle distribution and
other Psi angle distribution.

As you protein is 398 residues long, you can probably only focus on
functionally important residues and reweight their dihedral angle
distribution. A better way would be to reweight your PC distribution to
obtain free energy landscapes.

I hope this helps.


On Wed, Apr 17, 2019 at 2:49 AM Mayank Dixit <> wrote:

> Dear Users,
> I have performed accelerated molecular dynamics
> simulations (AMD) of protein in water by using dihedral boost and potential
> boost.
> I read the tutorial "
>". They are
> saying to select two dihedral angles among backbone atoms of three
> residues.
> Please let me know which three residues of protein (number of residues
> 398) I should select to reweight AMD results.
> Please help me in fixing this issue.
> Thanks and regards
> MD
> _______________________________________________
> AMBER mailing list

Best wishes
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Received on Wed Apr 17 2019 - 01:30:02 PDT
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