Subject: CCL:Amber Energies. What are they?

From: <[email-masked]>
Date: Mon, 06 Jun 1994 12:49:24 -0400 (EDT)

On Fri, 3 Jun 1994 [email-masked] wrote:

>AMBER 4.0 purports to output energies from MD runs in Kcals (pg 79 
>of the manual).  This energy does not seem to be kcals/mol, as a box
>of 200 water molecules gives twice the energy as a box of 100 molecules.

There is sometimes confusion about the energy unit "kcal/mol".  Its
use (as opposed to plain old kcal) allows us to work with numbers such
as 6.02 as opposed to 1.e-23.  Think of the unit kcal/mol as kcal/6.02e23
(i.e. the "/mol" is a scale factor, not a normalization factor).

The energy reported by AMBER is the total energy of the particular system
under consideration, and thus it makes sense that the energy of 200 water
molecules is about twice as much as the energy of 100 water molecules.

>My best guess is that since the AMBER code accepts a 'built-in' solvent
>such as TIP3p water as a single 'molecule' built up of many residues, the
>energies are reported in (kcal)/(mol of boxes of whatever).  Is this true?

No.  AMBER simply reports the total energy of the system.

We would run into some problems if AMBER and similar programs did try to
normalize the energies per mole, since the programs would first have to
answer the question "per mole of what: solute molecule, solvent molecule?"
Most of us would not like our software to be so presumptuous as to try to
answer this question.

>Also, has anyone had any difficulty using TIP4p water in AMBER?  The 
>pure solvent that I have run drops dramatically (~400 kcal) in energy 
>after about 30-40ps, and from there on fluctuates only about 1 kcal up or
>down in total energy.

The total energy *should* be constant.  The potential and kinetic energy
values should still be fluctuating, however.  If not, you are either running
your simulation at 0 Kelvin, or there is a genuine problem.

>It seems to have formed some type of rigid 
>'polywater'structure.  It has been suggested to me that this is caused by 
>the charge center being given a mass of ~12amu

There shouldn't be any problem with a mass of 12amu.

Regards,
Greg

====================================================================
Gregory King                             Internet: [email-masked]
Eastern Reg. Res. Ctr., ARS, USDA           Voice: (1) 215 233 6675
600 East Mermaid Lane                         Fax: (1) 215 233 6559
Philadelphia, PA  19118-2551
====================================================================