[gmx-users] freeze group gives Segmentation fault

Berk Hess gmx3 at hotmail.com
Tue Nov 11 08:34:01 CET 2008


I don't understand your mail.
Do you really get a segmentation fault, but also frames in your trajectory file?

I think I fixed the freezing of the whole system bug.
I tested it for a water system and it runs fine.

Maybe you have constraints in your system.
Asking your system to be completely frozen and to obey the constraints
is usually contradictory. Therefore you system might still move slightly
to try to obey the constraints.

Anyhow it seems pretty useless to me to simulate a completely frozen system.


> From: ilona.baldus at bioquant.uni-heidelberg.de
> Date: Mon, 10 Nov 2008 15:13:06 +0100
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] freeze group gives Segmentation fault
> I just tried Gromacs 4.0.2. It still gives a Segmentation fault:
> "Reading file topol.tpr, VERSION 4.0.2 (single precision)
> Loaded with Money
> Segmentation fault"
> I did a test, putting the whole system into one freezegroup. Then the  
> simulation starts running. But some of the atoms belonging to the  
> "freeze-group" still move: The RMSD keeps growing and the Potential  
> Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the  
> molecules moving. There is no pattern in the motion though. I checked  
> the index.ndx twice - there is no mistake in there.
> Ilona
> > There was a bug in the freeze group code that got fixed today. I  
> > don't know anything else about it. Please update your source code  
> > and try again.
> >
> > Mark
> > ilona.baldus at bioquant.uni-heidelberg.de wrote:
> >>
> >> Using freezegroups I get a Segmentation fault. The simulation does  
> >> not start, so the output is empty.
> >>
> >> "Reading file topol.tpr, VERSION 4.0_rc4 (single precision)
> >> Segmentation fault"

Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081111/e7b8bcdf/attachment.html>

More information about the gromacs.org_gmx-users mailing list