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

Wed Sep 30 17:10:54 CEST 2009

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
> >> > ---------------------------------------------------
> >> >
> >> > _______________________________________________
> >> > gmx-users mailing list gmx-users at gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > Please search the archive at http://www.gromacs.org/search before 
> >> posting!
> >> > Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-request at gromacs.org.
> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >> ------------------------------------------------------------------------
> >> See all the ways you can stay connected to friends and family 
> >> <http://www.microsoft.com/windows/windowslive/default.aspx>
> >> ------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before 
> >> posting!
> >> Please don't post (un)subscribe requests to the list. Use the www 
> >> interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> 
> 
> -- 
> ---------------------------------------------------
> 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
> ---------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090930/544e425e/attachment.html>