From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Mar 04 2014 - 19:14:15 CST
I cannot read the mind of the author of that statement, but my best guess
is that he or she meant to say that for many water models, the balance
between the electrostatic and the vdW components is such that you'll be
situated slightly up the wall when considering the interaction between
water molecules.
On 03/04/2014 07:24 PM, PANAGIOTA KYRIAKOU wrote:
> 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 <mailto:kyria008_at_umn.edu>
>
>
>
> On Tue, Mar 4, 2014 at 5:50 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> http://en.wikipedia.org/wiki/__Lennard-Jones_potential
> <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
> <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>
> <mailto:kyria008_at_umn.edu <mailto:kyria008_at_umn.edu>>
>
>
>
>
> Panagiota Kyriakou
>
> Graduate Student
>
> Dept. of Chemical Engineering and Materials Science
>
> University of Minnesota
>
>
> email: kyria008_at_umn.edu <mailto:kyria008_at_umn.edu>
>
>
>
> On Tue, Mar 4, 2014 at 5:50 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> http://en.wikipedia.org/wiki/__Lennard-Jones_potential
> <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
> <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>
> <mailto:kyria008_at_umn.edu <mailto:kyria008_at_umn.edu>>
>
>
>
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