Re: [AMBER] asking about mden

From: setyanto md <stwahyudi.md.gmail.com>
Date: Mon, 12 Mar 2012 17:26:43 +0700

Hi Ben,

Thank you for the respond.

Best regards,

Setyanto

On Mon, Mar 12, 2012 at 1:35 PM, Ben Roberts <ben.roberts.geek.nz> wrote:

> Hi Setyanto,
>
> On 12/03/2012, at 6:33 PM, setyanto md wrote:
>
> > Dear amber user and developer
> >
> > I've seen in mden file from my simulation
> >
> > <snip>
> >
> > I want to know about energy electrostatic.
> > 1. What is the different between E_14el and E_el ?
>
> E_14el is the electrostatic energy between atoms in a 1-4 topological
> relationship. In the chain of atoms A-B-C-D, where dashes are covalent
> bonds, A and D would be in a 1-4 relationship. E_el is the electrostatic
> energy between other atoms, except 1-2 and 1-3 pairs, for which pairwise
> electrostatic interactions are ignored. It is the sum of short-range
> electrostatics (up to a cutoff distance) and long-range electrostatics
> except for atoms in 1-4 relationships.
>
> > 2. How E_el being calculated when simulation ?
>
> Short-range electrostatics, up to a cutoff distance specified by the user
> (or, if not specified, a default value of I think 8 Angstroms), are
> computed using Coulomb's law. Long-range electrostatics are computed using
> the particle-mesh Ewald method, described in the references found in the
> Amber manual. 1-4 electrostatics are calculated the same way as others,
> then scaled; almost always, a 1-4 electrostatic interaction will be within
> the cutoff and therefore computed using Coulomb's law. If you need to know
> the algorithmic details, your best bet would be to look at the source code.
>
> > 3. I'd like to calculate the Energy Electrostatic between 2 residue, can
> I
> > use ptraj ? is there any tutorial for this calculation ?
>
> I suggest you look into energy decomposition. This is a function of Amber
> (more specifically, Sander, I think), and instructions can be found in the
> Amber manual.
>
> Hope that helps,
> Ben
>
>
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Received on Mon Mar 12 2012 - 03:30:02 PDT
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