[gmx-users] Dummies usage doubts
David van der Spoel
spoel at xray.bmc.uu.se
Thu Oct 11 13:02:29 CEST 2007
Jones de Andrade wrote:
> Hi Prof. David.
>
> What details do you mean? Actual topology files are attached. Anything else?
Is this a topology from pd2gmx or did you write it yourself?
Please check chapter 5 of the manual.
You want to check exclusions ánd start with one molecule.
>
> 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:
> > 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>
> > <mailto: 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>
> > <mailto:spoel at xray.bmc.uu.se
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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
> <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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--
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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