[gmx-developers] Possible bug in grompp?

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 19 08:47:32 CEST 2005

On Mon, 2005-04-18 at 16:43 -0600, Walter Ash wrote:
> I've been working on a new molecule topology and I've noticed what I 
> believe is a bug in grompp...  I am using the ffopls forcefield with 
> genpairs=yes, fudgeQQ and fudgeLJ = 0.5,  and combination rule 3.  This 
> is with the 3.2.1 distribution version.
> In the molecular topology, under [ pairs ], it appears I have to specify 
> LJ14 parameters in C6 and C12 format despite the use of sigma and 
> epsilon everywhere else in this forcefield (comb rule 3).  If I use 
> sigma and epsilon in a [ pairs ] definition, my LJ14 energies are orders 
> of magnitude too high as grompp intereprets these parameters as C6 and 
> C12 values instead.  Putting C6 and C12 parameters here gives the 
> expected behavior.
> This is contrary to what is stated in the manual and what I would expect 
> the behavior to be.
It seems that this was fixed recently for pair_types but I'm not sure
whether it was fixed for [ pairs ] as well. You could try the latest

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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