[gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?

[Justin A. Lemkul]

Thanks for the insights, Tsjerk.  I figured it was something to do with the new 
algorithm; just wanted to confirm that this was the expected behavior.

Indeed, trjconv is one's friend in such a case :)

-Justin

Tsjerk Wassenaar wrote:
> Hi Justin,
> 
> It's indeed the case that mdrun now writes broken molecules. Has to do
> with the domain decomposition and processors only keeping track of
> 'their' atoms. Too bad, but you'll just have to keep a .tpr around to
> make molecules whole again afterwards. Using trjconv -nojump with a
> suitable reference (not necessarily a .tpr) would also do it (and
> simultaneously remove the jumps...).
> 
> Cheers,
> 
> Tsjerk
> 
> On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Hi,
>>
>> I've been running some simulations with Gromacs 4.0 RC2, and I've noticed
>> something strange.  In the output .gro file at the end of a run, the
>> molecules in my system (a membrane protein) are broken, crossing periodic
>> boundaries. This affects the lipids at the periphery of the box, in my case.
>>
>> Has there been some change since the previous version that mdrun is now
>> writing broken molecules to fit everything within the unit cell?  Or is this
>> behavior unintentional?
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================