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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Received on Fri Aug 09 2013 - 08:00:03 PDT
