[gmx-users] Overriding "genpairs=yes" default for one specific molecule? Possible?

David spoel at xray.bmc.uu.se
Thu Apr 14 07:39:41 CEST 2005

On Wed, 2005-04-13 at 14:50 -0600, Walter Ash wrote:
> First, I am sorry if this has come up on the mailing list before - a 
> quick search didn't reveal anything obvious. 
> I am in a position where I would like to use a molecular topology in 
> conjuction with the OPLS-aa protein forcefield, but on first glance they 
> seem to be incompatible.  
> My problem is that OPLS uses genpairs=yes and fudgeLJ and fudgeQQ 
> parameters of 0.5.  I would like to override this behavior for this one 
> specific molecule - e.g. with exclusions.  However, after excluding the 
> automatic calculation of 1-4 non-bonded interactions I need to specify a 
> set of [pairs] to modify the dihedral functions.  Is this possible to do 
> with the OPLS defaults, or will I have to reparameterize my dihedral 
> functions for this molecule?
> Unfortunately the gromacs manual does not very specifically explain the 
> precedence of the different topology statements (e.g., do 'exclusions' 
> override 'pairs' or 'genpairs=yes' directive?  Or does genpairs=yes take 
> precedence over everything?).  My initial testing shows that the 
> topology is unstable if I attempt to first exclude all 1-4 interactions, 
> then define pairs, with genpairs=yes.
You can exclude as many bonded neighbors as you want for your molecule
(set right next to the molecule name). 1-4 Pairs have to be added
explicitly so that you have full control. Check e.g. and OPLS protein
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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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