Hi Golshan,
You are correct the internal terms should be identical - there is no
excuse for them not to be. I would caution that Gromacs uses KJ/mol and
not Kcal but the difference here is not 4.184 so it isn't a unit
conversion issue. It is also too big to be simple round off. Given the
structure is small you should be able to calculate it yourself by hand.
Make sure you are really doing just a single point energy calculation -
I.e. step 0 of a minimization for example and that you are not using shake
or anything else that might mess with the potential.
Then on a piece of paper you can iterate through with the coordinates you
have and calculate what all the bonds, angles and dihedrals should sum to.
It will likely take a couple of hours but you'll be able to convince
yourself what the correct value is.
This will tell you which code is correct. (I suspect AMBER). Suffice to
say the fact that Gromacs doesn't get this identical would cause me to be
VERY VERY suspicious. If one cannot get bonds, angles and dihedrals to
match then there is no hope for the code correctly implementing the force
field.
Note for the implementation of the Charmm force field in AMBER we get
these terms matching charmm to 10^-14 kcal/mol so there is no excuse.
http://www.rosswalker.co.uk/papers/Int_J_Quant_Chem_2009_109_15_3767-3772_C
hamber.pdf
All the best
Ross
On 8/8/13 12:26 PM, "Golshan Hejazi" <golshan.hejazi.yahoo.com> wrote:
>Hello everyone.
>
>I am doing some simple tests as following: I have an amber crd and top
>file. I perform an energy evaluation and I estimate the value of BOND,
>ANGLE and TORSION energies for a simple system (ace-ala-nme).
>
>Then I use amb2gmx.pl to convert the crd and top file to gromacs format
>and again I compute the BOND, ANGLE and TORSION energies of the same
>structure ...
>
>I expect to have identical values between gromacs and amber. However, the
>energis are not comparable.
>
> amber ... BOND= 0.0206 (kcal/mol) ANGLE=0.3620 (kcal/mol)
>TORSION=8.1071 (kcal/mol) gromacs .... BOND=0.14044 (kcal/mol)
>ANGLE=0.3780 (kcal/mol) TORSION=9.74190 (kcal/mol)
>
>I checked how amb2gmx converted the values of amber to gmx format. It
>seems to me that everything is correct. There is a factor of two
>difference between the force constants in amber and gromacs which I think
>in the energy calculation term ... it is already taken care of!
>
>So I see nothing wrong but ... energies dont match!
>Could you please help me to understan this
>
>Thanks
>Golshan
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Received on Thu Aug 08 2013 - 13:00:02 PDT
