[gmx-users] Dummies usage doubts
Jones de Andrade
johannesrs at gmail.com
Thu Oct 11 12:00:55 CEST 2007
Hi Prof. David.
What details do you mean? Actual topology files are attached. Anything else?
Thanks a lot in advance!
Sincerally yours,
Jones
On 10/11/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Thanks Prof. David.
> >
> > I've done all that now, but at the moment I'm locked getting lots of the
> > "lovelly" error:
> >
> > Warning: 1-4 interaction between 7 and 16 at distance 4.302 which is
> > larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding,
> > if not, you should increase table-extension in your mdp file
> > step 0Segmentation fault
>
> please give more details...
>
>
> >
> > I've visually checked the .gro file, and the atoms mentioned are not
> > from start at such crazy distances. I've included extra exclusions
> > between the virtual sites and the atoms that are at "one" and "two"
> > "bonds" away.
> >
> > Does it means I should include also the 1-4 in the exclusions or pair
> > sections? Sorry, never dealt with dummy sites before this. I thought
> > using a pre-equilibrated box with a different model would at least avoid
> > explosion problems, so or I missing something, of this assumption was
> > completelly wrong.
> >
> > Thanks a lot in advance,
> >
> > Sincerally yours
> >
> > Jones
> >
> > On 10/11/07, *David van der Spoel* <spoel at xray.bmc.uu.se
> > <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> > Jones de Andrade wrote:
> > > Hi all.
> > >
> > > Well, I'm having a bit of trouble here because the work has
> > decided to
> > > go in the direction of something I've never used before with
> gromacs:
> > > dummy atoms (or now "virtual sites").
> >
> > I assume this is not for a protein, in which case pdb2gmx does it
> > for you.
> > >
> > > I've got at least three questions in order to use them:
> > >
> > > 1 - does the virtual sites need to be included in the .gro files
> in
> > > order to make a simulation run?
> > >
> > Yes.
> >
> > > 2 - do I need to include them in the "exclusion list"?
> > It depends, but usually yes.
> >
> > >
> > > 3 - do I need to include them in the "atoms" section?
> > Yes.
> >
> > >
> > >
> > > Thanks a lot in advance for any help anyone can provide in these
> > > subjects. ;)
> > Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P
> etc.
> >
> >
> > >
> > > Sincerally yours,
> > >
> > > Jones
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> >
> > >
> > > _______________________________________________
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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
> > <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> > <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> >
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> >
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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