AMBER Archive (2003)

Subject: Re: your mail

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 21 2003 - 10:35:52 CST

On Tue, Jan 21, 2003, Anke Eisenmann wrote:
>
> I am wondering about several things in the Sander-output file:
>
> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 276.00 PRESS = 298.0
> Etot = -28036.8863 EKtot = 5186.3037 EPtot = -33223.1900
> BOND = 134.3085 ANGLE = 261.4501 DIHED = 360.3181
> 1-4 NB = 170.6899 1-4 EEL = -355.7682 VDWAALS = 4121.5170
> EELEC = -38083.3918 EHBOND = 0.0000 RESTRAINT = 167.6865
> EAMBER (non-restraint) = -33390.8765
> EKCMT = 2441.6776 VIRIAL = 1856.7857 VOLUME = 90915.1603
> Density = 1.0598
>
> 1. In which units is the VOLUME given?

Angstroms**3; see the FAQ entry on "units" at the Amber web page.

> 2. What are the 1-4 NB and 1-4 EEL terms for?

These are Lenneard-Jones and electrostatic interactions between atoms
separated by three covalent bonds. See any of the force field papers for
a discussion of this.

> 3. What does EKCMT mean?

It is the kinetic energy of the centers of masses of the molecules in the
system, used as an intermediate quantity in getting the virial, which in
turn is used to calculate the instantaneous pressure. It's not clear why
this is printed, since I don't think anybody ever looks at its value.

..dac 

-- 

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