[gmx-users] trjconv, -pbc whole, and Max OS X?

[Emma Falck]

Erik,

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 
same problem.

Emma

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?
> 
> Emma,
>
> 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.
>
> Cheers,
>
> Erik
>
> 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:
>>>> 
>>>> Hi,
>>>> 
>>>> My problem is with the trjconv command. I am trying to convert a
>>>> trajectory
>>>> 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
>>>> provided
>>>> on the gromacs pages.
>>>> 
>>>> Has anyone else had related/similar problems with trjconv, in
>> particular
>>>> with
>>>> OS X?
>>>> 
>>>> Best regards,
>>>> 
>>>> Emma
>>>> 
>>>> --
>>>> 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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