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

[Berk Hess]

Hi,

There are two separate issues here.

One is the charge groups assignment with AMBER.
I think that in Gromacs we, in general, do not want all atoms in separate charge groups,
but we want to include at least the hydrogens in a charge group with the heavy atom.
We would also like the option to make every atom a single charge group,
but pdb2gmx of 4.1 already has an option for this.
Since the AMBER force fields are currently not in the Gromacs package,
we don't have control over the charge group assignment.

The second issue is the crashing of the simulations.
I don't see why simulations would crash with the slightly strange charge group assignment.
But it sounds like there is a bug somewhere.
I suspect it could happen when an NH3 group is partially over a box edge.
This is strange though, since I think I check all nasty combinations of vsite generation
and charge groups.

I already got such a file from Bert.

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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