Why would you do
sum (ki*(r_i*r_i)) ??
That is not the correct equation. What you need is k*(r_i - r_re_i)**2, which is the difference between the actual bond lengths minus the equilibrium value.
On 8/9/13 10:53 AM, Golshan Hejazi wrote:
> This is for ALA to avoid any complication!
>
>
> [ bonds ]
> ; ai aj funct r k
> 1 2 1 1.0100e-01 3.6317e+05
> 3 4 1 1.0900e-01 2.8451e+05
> 5 6 1 1.0900e-01 2.8451e+05
> 5 7 1 1.0900e-01 2.8451e+05
> 5 8 1 1.0900e-01 2.8451e+05
> 1 3 1 1.4490e-01 2.8200e+05
> 3 5 1 1.5260e-01 2.5941e+05
> 3 9 1 1.5220e-01 2.6527e+05
> 9 10 1 1.2290e-01 4.7698e+05
>
> >From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) = 42536.87 (kj/mol)
> however, when I perform a rerun on the gro file ... this is the bond energy: 2.20074e-01 (kj/mol) in gromacs
> and 0.0003 (kcal/mol) from amber
>
>
>
> ________________________________
> From: David A Case <case.biomaps.rutgers.edu>
> To: Golshan Hejazi <golshan.hejazi.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Friday, August 9, 2013 9:46 AM
> Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs
>
>
> On Fri, Aug 09, 2013, Golshan Hejazi wrote:
>> I computed the BOND and ANGLE energies. But it is only increasing my
>> confusion ... Look: I have a simple ace-ala-nme system.
> How about going to just ace-nme? It would much easier to compare each
> individual term, and you would still have bonds, angles and dihedrals.
>
> While I am thinking about it, be sure that the conversion of the blocking
> groups (ace and nme) between Amber and Gromacs is correct (i.e. not just
> the amino acids themselves.)
>
> ...dac
>
>
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Aug 09 2013 - 08:30:03 PDT
