[gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)

[David van der Spoel]

Berk Hess wrote:
> 
> 
>  > Date: Tue, 27 Jan 2009 08:46:35 +0100
>  > From: spoel at xray.bmc.uu.se
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] Segmentation fault with genbox -nmol 
> (version 4.0.3)
>  >
>  > Justin A. Lemkul wrote:
>  > >
>  > > Hi All,
>  > >
>  > > I'm building a system consisting of a protein complex with a few 
> ligands
>  > > free in solution at the outset of the simulation. I'm using genbox -ci
>  > > -nmol to insert the ligands prior to solvation. I'm using version 
> 4.0.3
>  > > on a dual-core Intel MacBook. The following command fails:
>  > >
>  > > genbox -cp complex_newbox.gro -ci lig.gro -nmol 10
>  > >
>  > > The command works, however, for values of -nmol < 4. The command with
>  > > -nmol 10 works on another machine, an AMD64 Ubuntu box, so this 
> problem
>  > > appears specific to my Mac. Using genbox from version 3.3.3 works just
>  > > fine on the MacBook, and both 4.0.3 and 3.3.3 were built using the 
> same
>  > > compilers (gcc suite, version 4.0.1).
>  > >
>  > > The last few lines of genbox.log from -debug 1 are:
>  > >
>  > > No fcdata or table file name passed, can not read table, can not do
>  > > bonded interactions
>  > > Going to determine what solvent types we have.
>  > >
>  > > ...in case that's helpful. Any ideas why this may have broken, or why
>  > > it may be specific to my Mac?
>  > >
>  > >
>  > > Thanks,
>  > > Justin
>  > >
>  > please enter a bugzilla for this.
> 
> I just ran valgrind on genbox 4.0.4_pre.
> I get a uninit value warning in check_solvent_cg.
> I fixed two issues in this part of the code, so it could be that
> 4.0.4 has less problems than 4.0.3.
> But looking at do_nsgrid it seems that genbox still does not
> calculate overlap between the inserted molecules,
> although the output says it does.
> 
> What does genbox do?

Drag around a lot of history.

There is also a problem with vsites, waters are put in place of vsites 
but this could be due to other problems (archaic gromos-centric input 
files).

> 
> Berk
> 
>  >
>  > --
>  > David van der Spoel, Ph.D., Professor of Biology
>  > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>  > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>  > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>  > _______________________________________________
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://www.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! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se