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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
> <mailto: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> 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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>
> >
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> --
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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
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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