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

[Jochen Hub]

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
---------------------------------------------------