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

Jochen Hub jochen at xray.bmc.uu.se
Fri Oct 2 12:30:03 CEST 2009 

Great, thanks a lot!

Jochen


Berk Hess wrote:
> I finally managed to track down the bug with the charge group assignment.
> I turned out to be in specific code that hardcoded renames H1, H2 and H3
> to H in the N-terminus only when matching atoms to the topology
> (the horrendous pdb2gmx again...).
>
> I fixed it for 4.0.6 and 4.1.
> But this will have very little effect on simulations, only AMBER with 
> v-sites
> simulations will crash, due to the combination with the other bug I fixed.
> And the amber vsite files are not officially released.
>
> Berk
>
> > Date: Thu, 1 Oct 2009 15:13:04 +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
> >
> > Berk Hess wrote:
> > > Hi,
> > >
> > > I just ran pdb2gmx (4.0.5 and git master) with AMBER on a test 
> di-peptide.
> > > But for me all H's in the NH3 terminus always end up in different
> > > charge-groups.
> > > No matter if I use v-sites or not and if use -ignh or not.
> > > So I don't understand how you managed to get the H's in the same
> > > charge group.
> > Weird, I always get the H's in separate charge groups. I tried with
> > older and newer pdb2gmx, amber03, amber99sb. I and compared with some
> > older stuff from 1-2 years ago. I had the H's in the terminal always in
> > separate charge groups...
> >
> > But I don't think it will make a difference, so I'll just stick to 
> these
> > CGs.
> >
> > Btw, the bug seemed to have fixed the problem, the simulations running
> > now for a couple of ns. So thanks again for the bugfix.
> >
> > Jochen
> >
> >
> >
> > >
> > > Berk
> > >
> > > > Date: Wed, 30 Sep 2009 18:14:06 +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
> > > >
> > > > 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?
> > > > Ah, you're right. One of the CG which caused the crash is the
> > > following,
> > > > with 2 H's in one CG:
> > > >
> > > > 1 amber99_39 1 NPRO N 1 -0.202 16.026 ;
> > > > qtot -0.202
> > > > 2 amber99_17 1 NPRO H1 2 (!) 0.312
> > > > 0 ; qtot 0.11
> > > > 3 amber99_17 1 NPRO H2 2 (!) 0.312 0
> > > > ; qtot 0.422
> > > > 4 amber99_11 1 NPRO CD 3 -0.012 14.026 ;
> > > > qtot 0.41
> > > >
> > > > Note however, that the CG which also caused crashes was 
> different, with
> > > > 2 vsites and 1 heavy atom in the same group, plus a separate CG 
> with 3
> > > > hydrogens. According to the lincs warning and 1-4 distance 
> error, the
> > > > hydrogens seemed to be involved. Typically the warning/error 
> mentioned
> > > > the hydrogen to have moved/rotated too much:
> > > >
> > > > 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
> > > >
> > > > >
> > > > > 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 will get the lates gmx with your bugfix and write back if the 
> crashes
> > > > still appear.
> > > >
> > > > >
> > > > > 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.
> > > > I don't understand that either. The result is the same no matter 
> if I
> > > > use -ignh, or if the hydrogens are present in the input gro file or
> > > not.
> > > > For examle, using
> > > >
> > > > pdb2gmx -f asn[-h].gro -ff amber99sb [-ignh]
> > > >
> > > > with asn-h.gro or asn.gro are just the ASN at the N-terminus 
> (with or
> > > > without hydrogens), e.g. asn-h.gro:
> > > >
> > > > Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> > > > 8
> > > > 97NASN N 1423 0.062 -1.317 1.235
> > > > 97NASN CA 1427 0.109 -1.209 1.154
> > > > 97NASN CB 1429 0.233 -1.249 1.073
> > > > 97NASN CG 1432 0.213 -1.368 0.981
> > > > 97NASN OD1 1433 0.263 -1.478 1.005
> > > > 97NASN ND2 1434 0.143 -1.345 0.867
> > > > 97NASN C 1437 0.003 -1.148 1.068
> > > > 97NASN O 1438 0.033 -1.090 0.964
> > > > 0.00000 0.00000 0.00000
> > > >
> > > > The written topology is:
> > > >
> > > > [ atoms ]
> > > > ; nr type resnr residue atom cgnr charge mass
> > > > typeB chargeB massB
> > > > 1 amber99_39 1 NASN N 1 0.1801 14.01 ;
> > > > qtot 0.1801
> > > > 2 amber99_17 1 NASN H1 2 0.1921 1.008 ;
> > > > qtot 0.3722
> > > > 3 amber99_17 1 NASN H2 2 0.1921 1.008 ;
> > > > qtot 0.5643
> > > > 4 amber99_17 1 NASN H3 2 0.1921 1.008 ;
> > > > qtot 0.7564
> > > > 5 amber99_11 1 NASN CA 3 0.0368 12.01 ;
> > > > qtot 0.7932
> > > > 6 amber99_28 1 NASN HA 4 0.1231 1.008 ;
> > > > qtot 0.9163
> > > > ...
> > > >
> > > > Weird. The same thing happens by the way with a proline 
> N-terminus, no
> > > > matter if hydrogens are present before pdb2gmx or not.
> > > >
> > > > So thanks a lot for the help,
> > > >
> > > > Jochen
> > > >
> > > > >
> > > > > 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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> > --
> > ---------------------------------------------------
> > 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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