[gmx-users] Dummies usage doubts
Jones de Andrade
johannesrs at gmail.com
Thu Oct 11 08:42:23 CEST 2007
Thanks Prof. David.
I've done all that now, but at the moment I'm locked getting lots of the
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
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
Thanks a lot in advance,
On 10/11/07, David van der Spoel <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?
> > 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?
> > 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 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://folding.bmc.uu.se
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