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

[Erik Lindahl]

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