[gmx-developers] Accessing forcefield data

[David]

On Thu, 2004-07-08 at 18:02, Martin Ulmschneider wrote:
> Thanks, i worked it out. Now i would like to access the c6 and c12 
> values from the Lenard Jones (vdW) interaction. Could you point me to 
> the right routine? I've looked at mk_nbfp in force.c, which i think has 
> the cross terms for all atomtypes, but how can i find the values for 
> some atom j?
You index the matrix with the atom type in mdatoms->type
> 
> Many thanks in advance!
> Best wishes,
> Martin
> 
> David wrote:
> > On Tue, 2004-07-06 at 23:17, Martin Ulmschneider wrote:
> > 
> >>Hi,
> >>
> >>I am adding an extra force in gromacs. This force depends on the 
> >>forcefield values of r0 and angle0 (i.e. the forcefield bondlength and 
> >>angle). Hence i would prefer to access r0 and angle0 in the CODE rather 
> >>than writing a new forcefield file loader. Is this very difficult to access?
> > 
> > Not very...
> > There is a Urey-Bradley term in the bonded forces which should have all
> > the information you need. (src/gmxlib/bondfree.c)
> > 
> > 
> >>Best wishes,
> >>Martin
> >>
> >>David wrote:
> >>
> >>>On Tue, 2004-07-06 at 21:41, Martin Ulmschneider wrote:
> >>>
> >>>
> >>>>Hi,
> >>>>
> >>>>I would like to check the forcefield data (i'm interested in the 
> >>>>forcefield bond lengths r0 and angles alpha0) in gromacs. Could you 
> >>>>please tell me which structure they are in and how i can access them? 
> >>>>E.g. the mass of atom j can be accessed by  mass = top->atoms.atom[j].m. 
> >>>>Is there a simlar way to access b0 and alpha0?
> >>>>
> >>>
> >>>wouldn't you rather browse through the text files in share/top ?
> >>>otherwise you'll have to decipher the idef structure of the topology.
> >>>
> >>>
> >>>>Many thanks!!!
> >>>>Martin
> >>>>
> >>>>_______________________________________________
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> >>
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> 
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-- 
David.
________________________________________________________________________
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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