Re: VDW energy: positive or negative?

From: PANAGIOTA KYRIAKOU (kyria008_at_gmail.com)
Date: Tue Mar 04 2014 - 18:24:54 CST

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Thank you

My question was mostly generated by the following statement in the post:

"many water models are built with their VDW energy repulsive at the total
energy minimum"

However when I checked the parameter files I use ( CHARMM 36), the epsilon
values are negative, so the statement above is not true.

I was wondering under what conditions this can be true, since it could
simply justify the positive sign of the total VDW energy..

Giota

Panagiota Kyriakou

Graduate Student

Dept. of Chemical Engineering and Materials Science

University of Minnesota

email: kyria008_at_umn.edu

On Tue, Mar 4, 2014 at 5:50 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:

> http://en.wikipedia.org/wiki/Lennard-Jones_potential
> See that steep repulsive wall on the left side? Basically, attractive
> electrostatic forces can, and in many cases will, pull the system a little
> bit up that wall, into the positive region.
>
> And that's all I have to say about that.
>
>
>
> On 03/04/2014 06:20 PM, PANAGIOTA KYRIAKOU wrote:
>
>> Hello,
>>
>> I was wondering if someone could give me a rigid and detailed explanation
>> of why the VDW energy is positive in many systems (while the total energy
>> is negative), such as a protein in a solvated box? I read at a previous
>> post that it is related to the water model
>> (http://www.ks.uiuc.edu/Research/namd/mailing_list/
>> namd-l.2005-2006/3358.html).
>>
>> Could someone provide some more details on this issue?
>>
>> This is a general question and not specific to a simulation run , so this
>> is why I am not including any input/output files.
>>
>> Giota
>>
>> Panagiota Kyriakou
>>
>> Graduate Student
>>
>> Dept. of Chemical Engineering and Materials Science
>>
>> University of Minnesota
>>
>>
>> email: kyria008_at_umn.edu <mailto:kyria008_at_umn.edu>
>>
>>
>