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

Jochen Hub jochen at xray.bmc.uu.se
Wed Sep 30 18:24:44 CEST 2009 

Ups, sorry, the other CG which caused the crashes (with 3 H's) was of 
course also in your category and not "different". I think I should go 
home for today... :-)

So thanks again for the bugfix!

Jochen


Berk Hess wrote:
> Hi,
>
> Are you 100% sure you have no other charge groups in your system
> that consist of only virtual sites, but at least with 2 virtual sites?
>
> I just fixed a bug with this situation for 4.0.6 and 4.1.
> You can try the git master or 4.0 release branch.
>
> I don't understand why only your terminal NH3 becomes a single charge 
> group,
> unless the hydrogens were generated with the .hdb file,
> while they were present for all other NH3 groups.
>
> Berk
>
> > Date: Wed, 30 Sep 2009 16:45:39 +0200
> > From: jochen at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, 
> and crashes
> >
> > Hey Berk,
> >
> > I just found that the simulation with a separate CG on each atom also
> > crashed, but much later (after 11ns), that why I just noticed that. I
> > have repeated the simulations now to make really sure that the crashes
> > are reproducible.
> >
> > Jochen
> >
> >
> > Jochen Hub wrote:
> > >
> > > 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
> > ---------------------------------------------------
> >
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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
---------------------------------------------------

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