AMBER Archive (2005)

Subject: Re: AMBER: force constant Unit used in TMD

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Apr 04 2005 - 11:06:45 CDT

 the energies reported by Amber are in units of per mole.
Nothing is per molecule. This goes for the force constants as well.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

xhu1_at_memphis.edu wrote:

>Dear Amber users,
>
>I have a question about Targeted MD: what's the unit of force constant
>used in TMD, kcal/(molecule*A^2) or kcal/(mole*A^2)? according to the
>energy term: E=0.5* TGTMDFRC * NATTGTRMS * (RMSD-TGTRMSD)**2, it
>should be kcal/(molecule*A^2). Am I right? Sorry for this simple
>question. Thank you very much!
>
>Best
>
>Shawn
>
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