[gmx-developers] Re: Accessing forcefield data

[Jason DeJoannis]

The non-bonded interactions are buried in the mysterious
inner loops so it can be difficult to find an example.

Here is what I do:

C6(fr->nbfp,  fr->ntype, i, j)
C12(fr->nbfp, fr->ntype, i, j)

where i & j are atom types which can be obtained from

i = top->atoms.atom[k].type
j = top->atoms.atom[l].type

for atoms k & l.


---
Jason de Joannis, Ph.D.
Chemistry Department, Emory University
1515 Pierce Dr. NE, Atlanta, GA 30322
Phone: (404) 712-2983
Email: jdejoan at emory.edu
http://userwww.service.emory.edu/~jdejoan



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>    1. Re: Accessing forcefield data (Martin Ulmschneider)
>    2. Re: Accessing forcefield data (David)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 08 Jul 2004 18:02:57 +0200
> From: Martin Ulmschneider <ulmschne at caspur.it>
> Subject: Re: [gmx-developers] Accessing forcefield data
> To: Discussion list for GROMACS development
> 	<gmx-developers at gromacs.org>
> Message-ID: <40ED7031.5010907 at caspur.it>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
> 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?
>
> 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
> >>>>
> >>>>_______________________________________________
> >>>>gmx-developers mailing list
> >>>>gmx-developers at gromacs.org
> >>>>http://www.gromacs.org/mailman/listinfo/gmx-developers
> >>>>Please don't post (un)subscribe requests to the list. Use the
> >>>>www interface or send it to gmx-developers-request at gromacs.org.
> >>
> >>_______________________________________________
> >>gmx-developers mailing list
> >>gmx-developers at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-developers
> >>Please don't post (un)subscribe requests to the list. Use the
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>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 08 Jul 2004 19:56:57 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] Accessing forcefield data
> To: Discussion list for GROMACS development
> 	<gmx-developers at gromacs.org>
> Message-ID: <1089309417.5102.0.camel at h176n2fls34o1123.telia.com>
> Content-Type: text/plain
>
> 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
> > >>>>
> > >>>>_______________________________________________
> > >>>>gmx-developers mailing list
> > >>>>gmx-developers at gromacs.org
> > >>>>http://www.gromacs.org/mailman/listinfo/gmx-developers
> > >>>>Please don't post (un)subscribe requests to the list. Use the
> > >>>>www interface or send it to gmx-developers-request at gromacs.org.
> > >>
> > >>_______________________________________________
> > >>gmx-developers mailing list
> > >>gmx-developers at gromacs.org
> > >>http://www.gromacs.org/mailman/listinfo/gmx-developers
> > >>Please don't post (un)subscribe requests to the list. Use the
> > >>www interface or send it to gmx-developers-request at gromacs.org.
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
> --
> 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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