Berk Hess wrote:
> Date: Tue, 27 Jan 2009 08:46:35 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@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.
> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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--
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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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