[gmx-users] trjconv, -pbc whole, and Max OS X?
efalck at cc.hut.fi
Thu Nov 17 23:45:34 CET 2005
I was wrong about the first frame. When I look at my .trr file
using ngmx, then all lipids in all frames are whole, as they should. It
is only when I look at my .gro file -- either with ngmx or vmd -- when I
see broken lipids in most of the frames. This .gro file I have generated
with trjconv using the -pbc whole option. This does not seem to
restrict itself to Mac OS X -- I checked with RedHat, and ran into the
On Thu, 17 Nov 2005, Erik Lindahl wrote:
> Date: Thu, 17 Nov 2005 23:22:26 +0100
> From: Erik Lindahl <lindahl at sbc.su.se>
> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] trjconv, -pbc whole, and Max OS X?
> Are you sure your individual molecules (single lipids) are broken into parts?
> mdrun never writes broken molecules, but the periodic image is determined so
> the first atom of each molecule is inside the box and no periodicity jumps
> occur inside a molecule.
> There are a couple of other -pbc options in case you want to force all atoms
> inside the box (break molecules) or to keep a membrane more intact.
> On Nov 17, 2005, at 10:58 PM, Emma Falck wrote:
>> The first frame seems to contain broken lipids, too. I thought trjconv
>> would make the lipids whole irrespective of this, but apparently this is
>> not the case. What should I do?
>>> What about the initial structure of the run?
>>> On 11/17/05, Emma Falck <efalck at cc.hut.fi> wrote:
>>>> My problem is with the trjconv command. I am trying to convert a
>>>> in the .trr format to a trajectory in the .gro format, such that the
>>>> molecules are whole in the resulting trajectory. To do so, I use trjconv
>>>> with the option '-pbc whole'. Even so, my molecules -- both lipids and
>>>> water molecules -- are broken in the resulting .gro file.
>>>> I recently installed Gromacs 3.3 to my PowerBook, that runs OS X 10.4.
>>>> I did not compile Gromacs from the source, but used the OS X package
>>>> on the gromacs pages.
>>>> Has anyone else had related/similar problems with trjconv, in
>>>> OS X?
>>>> Best regards,
>>>> Dr. Emma Falck
>>>> Beckman Institute, UIUC
>>> Viswanadham Sridhara,
>>> Graduate Research Assistant,
>>> Old Dominion University, "VIRGINIA".
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> Erik Lindahl <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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