AMBER Archive (2005)

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

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Apr 04 2005 - 11:53:23 CDT

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_at_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_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
>>>
>>>------------------------------------------------------------------
>>>
>>-----
>>
>>>The AMBER Mail Reflector
>>>To post, send mail to amber_at_scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>
>>>
>>>
>>-------------------------------------------------------------------
>>----
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
===================================================================
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_at_sunysb.edu
=================================================================== 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu