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

[Emma Falck]

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".