[gmx-users] OPLS-AA Coulomb-14 energies incorrect!

[David]

On Wed, 2003-08-06 at 08:59, Malcolm Gillies wrote:
> Hi,
> 
> I appear to have found an error in the calculation of the Coulomb 1-4
> energies using the GROMACS OPLS-AA implementation. Have potential
> energies calculated with this force field been validated against those
> from some other implementation (e.g. BOSS, MCPRO, Impact, MacroModel
> etc)?
> 
> The Coulomb (SR) component of the GROMACS energy agrees with the
> corresponding energy from TINKER (i.e. as calculated by setting
> chg-14-scale to 0.0), but the Coulomb-14 energy is out by a sizeable
> percentage. i.e for the attached file GROMACS reports 224.739 kJ/mol
> while TINKER reports 258.3687 kJ/mol.
I've found the source of the error: the interactions between the
N-terminal hydrogens and the HA* are not listed in the pair interaction
list. When you do so the energies are identical. (see atached modified
gro file and test.pl script).

I've checked for another OPLS topology that I had lying around and found
- for the N-terminus it is incorrect there as well
- in general 14 interactions between H's are turned off (they are
treated as normal interactions).

However pdb2gmx has a flag -H14 which turns on 1-4 interactions between
H atoms. It seems therefore that OPLS calculations need to be performed
with this option:

pdb2gmx -H14 [ more flags ]

(in a single test on a pdb file I find that the HH 1-4 interactions are
indeed listed when the flag is used)

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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S  C  A  M  O  R  G
   10
    1GLY      N    1   0.442   0.702  -0.555    -0.3 
    1GLY     H1    2   0.470   0.621  -0.607    0.33 
    1GLY     H2    3   0.456   0.685  -0.457    0.33 
    1GLY     H3    4   0.345   0.721  -0.572    0.33 
    1GLY     CA    5   0.522   0.816  -0.596    0.09 
    1GLY    HA1    6   0.628   0.792  -0.578    0.06 
    1GLY    HA2    7   0.509   0.832  -0.704    0.06 
    1GLY      C    8   0.490   0.946  -0.524     0.7 
    1GLY     O1    9   0.391   0.942  -0.430    -0.8 
    1GLY     O2   10   0.563   1.056  -0.559    -0.8 
   0.28265   0.43423   0.27368
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