[gmx-users] Dummies usage doubts

[David van der Spoel]

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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-- 
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