[gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

[Jochen Hub]

I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else?

Jochen


Berk Hess wrote:
> Hi,
>
> One question:
> Are these crashes single processor, with domain decomposition, or both?
>
> Berk
>
> > Date: Wed, 30 Sep 2009 15:35:42 +0200
> > From: jochen at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and 
> crashes
> >
> > Hi,
> >
> > I have been trying to use vsites with AMBER99SB, but the simulation
> > frequently cashes after a few hundred ps with the suspects (lincs
> > warnings, 1-4 distance error). I could pinpoint the problem to 
> erroneous
> > charge group assignments generated by pdb2gmx at the NH3 group at the
> > N-terminus. The following charge group assignments caused the error:
> >
> > ; nr type resnr residue atom cgnr charge mass
> > 1 MNH3 1 NASN MN1 1 0 8.517 ;
> > qtot 0
> > 2 MNH3 1 NASN MN2 1 0 8.517 ;
> > qtot 0
> > 3 amber99_39 1 NASN N 1 0.1801 0 ;
> > qtot 0.1801
> > 4 amber99_17 1 NASN H1 2 0.1921 0 ;
> > qtot 0.3722
> > 5 amber99_17 1 NASN H2 2 0.1921 0 ;
> > qtot 0.5643
> > 6 amber99_17 1 NASN H3 2 0.1921 0 ;
> > qtot 0.7564
> > 7 amber99_11 1 NASN CA 3 0.0368 13.018 ;
> > qtot 0.7932
> > ...
> >
> > The NH3 groups in the lysines were fine and did not cause any error. 
> The
> > only difference compared to the N-terminus is that each of the three H
> > in the NH3 has its own charge group, but the vsites and the N are still
> > in the same CG:
> >
> > 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ;
> > qtot 0.9937
> > 31 amber99_28 2 LYP HE1 30 0.1135 0 ;
> > qtot 1.107
> > 32 amber99_28 2 LYP HE2 31 0.1135 0 ;
> > qtot 1.221
> > 33 MNH3 2 LYP MNZ1 32 0 8.517 ;
> > qtot 1.221
> > 34 MNH3 2 LYP MNZ2 32 0 8.517 ;
> > qtot 1.221
> > 35 amber99_39 2 LYP NZ 32 -0.3854 0 ;
> > qtot 0.8353
> > 36 amber99_17 2 LYP HZ1 33 0.34 0 ;
> > qtot 1.175
> > 37 amber99_17 2 LYP HZ2 34 0.34 0 ;
> > qtot 1.515
> > 38 amber99_17 2 LYP HZ3 35 0.34 0 ;
> > qtot 1.855
> >
> > Alternatively, I have also tried to give every single atom (including
> > the vsites MN??) a separate charge group, which also worked fine.
> >
> > 1)
> > So, is there any reason why the dummies should be in the same CG as the
> > nitrogen? Or should it be fine just to assign a separate CG to every 
> atom?
> >
> > 2)
> > Is a bug report appreciated on that issue?
> >
> > Best,
> >
> > Jochen
> >
> >
> > --
> > ---------------------------------------------------
> > Dr. Jochen Hub
> > Molecular Biophysics group
> > Dept. of Cell & Molecular Biology
> > Uppsala University. Box 596, 75124 Uppsala, Sweden.
> > Phone: +46-18-4714451 Fax: +46-18-511755
> > ---------------------------------------------------
> >
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-- 
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---------------------------------------------------