Dear Adrian,
Thanks for the correction. I computed by hand!!!! for amber and gromacs the BOND energy of ALA according to amber topology.
Here is the results:
GROMACS:
The number that I obtained: .440148 (kj/mol)
The number in the gromacs log file: .220074 (kj.mol)
There is a factor of 2 difference ... which I think it is correct ... and they take care of it in the energy file.
AMBER:
The number that I obtained: .052598574280 (kcal/mol)
The number in the AMBER mdout file: 0.0003 (kcal/mol)
What is really the correct value? I think .220074 (kj.mol) is the correct value ... because when I convert it to kcal/mol ... I arrive to the same number .052598574280 (kcal/mol) ... that I obtained by manually computing the BOND energy for amber.
I attached some files if you wish to control it. There is crd and top file of amber, gro and top file of gromacs and another file(called test) which contains to make it easier for you to check:
r_eq r(distance of the atom according to amber.coor) k(gromacs) k(amber)
What do you think?
G.
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
To: Golshan Hejazi <golshan.hejazi.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, August 9, 2013 11:05 AM
Subject: Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs
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 - 10:30:02 PDT
