Thank you very much, Viktor!!! the orignal one is what I want.
Best
Shawn
----- Original Message -----
From: Viktor Hornak <hornak.csb.sunysb.edu>
Date: Monday, April 4, 2005 11:53 am
Subject: Re: AMBER: force constant Unit used in TMD
>
> If you need a paper that describes TMD method implemented in
> AMBER7 (and
> 8), here is the original reference (it's slightly different from
> original TMD method proposed by Schlitter):
>
> Apostolakis J., Ferrara P, Caflisch A: Calculation of
> conformational
> transitions and barriers in solvated systems: Application to the
> alanine
> dipeptide in water.
> J. Chem. Phys. 110(4), p. 2099 (1999)
>
> If you're looking for papers that used AMBER implementation of
> TMD, I've
> seen a few but don't have specific references handy...
>
> Cheers,
> -Viktor
>
> xhu1.memphis.edu wrote:
>
> >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.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.stonybrook.edu
> >>===================================================================
> >>
> >>
> >>
> >>
> >>xhu1.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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>
> --
> ===================================================================
> Viktor Hornak
> Center for Structural Biology Phone: (631)632-1439
> SUNY at Stony Brook Fax: (631)632-1555
> Stony Brook, NY 11794-5115 E-mail: viktor.hornak.sunysb.edu
> ===================================================================
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Received on Mon Apr 04 2005 - 18:53:02 PDT
