Re: [AMBER] asking about mden

From: Ben Roberts <ben.roberts.geek.nz>
Date: Mon, 12 Mar 2012 19:35:11 +1300

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 - 00:00:03 PDT
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