Re: Re: high vdw energy

From: AYTUG TUNCEL (ATUNCEL_at_KU.EDU.TR)
Date: Fri Dec 01 2006 - 09:38:34 CST

I used TIP3 water. can you clarify what do you mean by "many water models are built with their vdW
energy repulsive at the total energy minimum", do you mean that the negative contribution is coming dominantly from water molecules? thanks.

aytug

-----Original Message-----
From: Xiongce Zhao <zhaox_at_ornl.gov>
To: AYTUG TUNCEL <ATUNCEL_at_KU.EDU.TR>
Date: Fri, 01 Dec 2006 08:44:12 -0500
Subject: Re: namd-l: high vdw energy

what water model do you use? many water models are built with their vdW
energy repulsive at the total energy minimum. In NAMD, vdW and
electrostatics are separately calculated, which may result in pure
positive vdW energy. But the total energy (elec+vdW) should be negative.

On Thu, 2006-11-30 at 17:44, AYTUG TUNCEL wrote:
> Dear all,
>
> I have a two chain (receptor = 452, ligand = 451 residue) protein explicit solvent, 5ns simulation. When I look to the .out file I see that even the electrostatic energy is very negative (-351813.6281) the vdw energy is very high, it is 25662.5684. These values are from the last frame. Is this kind of high vdw value normal or is it too high? or is it related to the size of the system. thanks in advance.
>
> aytug
>
>

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