[gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 5 21:02:18 CEST 2008
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 :)
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...).
> On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> 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 A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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