AMBER Archive (2006)

Subject: Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Thu Jan 12 2006 - 16:10:58 CST

I'm confused by your use of the term "e&s".
electrostatics are not calculated for 1-1, 1-2 and 1-3.
As you say, 1-2 and 1-3 are in bond and angle terms.
1-4 are calculated separately from others and have a scaling
factor. For GB solvation, all pairs are included.
hope that helps
Carlos

Ilyas Yildirim wrote:

>Dear Carlos,
>
>Thanks for your response. The reason why I asked the question is to see
>where and how the e&s interaction is used. I thought that the e&s energy
>included all the e&s interactions; 1-2, 1-3, 1-4, etc... But I think that
>this is not the case in AMBER force field. The 1-2, 1-3 e&s interactions
>are incorporated in the bond and angle terms.
>
>So, in reality, the meaning of e&s interaction in AMBER force field is
>including the 1-4, 1-5, 1-6, etc. interactions and the e&s intermolecular
>interactions, is that right?
>
>Best,
>
>On Thu, 12 Jan 2006, Carlos Simmerling wrote:
>
>
>
>>>After minimization, the .out file has the decomposed energies for each
>>>step, such as BOND, ANGLE, DIHED, VDWAALS, EEL, HBOND, 1-4 VDW, 1-4 EEL,
>>>RESTRAINT, etc. As far as I understood, EEL is the electrostatic energy,
>>>which excludes the electrostatic energies of the 1-4 interactions, am I
>>>right?
>>>
>>>
>>>
>>yes
>>
>>
>>
>>>If yes, what is the importance of 1-4 EEL?
>>>
>>>
>>>
>>what do you mean by "importance"? they are interactions between
>>atoms separated by 3 bonds (1-4 pairs).
>>
>>
>>
>>>And the same goes for
>>>VDWALLS energy; what would be the importance of the 1-4 VDW?
>>>
>>>
>>>
>>>
>>>
>>same as 1-4 EEL but for vdw.
>>if these don't answer the questions then let us know more specifically
>>what you mean.
>>
>>
>>
>>>Best,
>>>
>>>
>>>
>>>
>>>
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>
>
>

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