AMBER Archive (2005)

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

From: xhu1_at_memphis.edu
Date: Mon Apr 04 2005 - 11:33:01 CDT

Thank you very much, Dr. Simmerling! Have you any suggestion about
reference of TMD using in AMBER? I can't find it in the manual. ThankS
again.

Regards

Shawn

----- Original Message -----
From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
Date: Monday, April 4, 2005 11:06 am
Subject: Re: AMBER: force constant Unit used in TMD

> 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/carlosStony 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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