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

[Emma Falck]

I just installed gromacs 3.2.1 to my system. Here trjconv with the option 
-pbc whole works exactly as I would expect it to, ie, leaves the molecules 
whole/intact. I am using exactly the same syntax as I used with the 3.3 
version.

Emma

On Fri, 18 Nov 2005, Emma Falck wrote:

> Date: Fri, 18 Nov 2005 00:45:34 +0200 (EET)
> From: Emma Falck <efalck at cc.hut.fi>
> 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?
> 
> 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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