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

[Berk Hess]

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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