[gmx-users] broken molecules in ouput of MDRUN

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 6 02:15:39 CEST 2009

Gurpreet Singh wrote:
> Dear Users,
> I am simulating a binary mixture of cyclohexane-water using gromacs
> 4.0.4. Every thing works fine except that the output trajactory (.xtc
> file) contains broken molecules. 
> 	Interestingly enough, as the last frame of simulation is also dumped as
> gro file, has all the molecules as a whole, where as same frame in xtc
> file(the last frame) is broken.
> I searched the mailing list and found out that few other users have also
> complained about it.
> http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

This link is the Search page :)  Open the frame in a new window; copy that link 
when referring to archived posts.

> Does this mean that I have to run trjconv after every simulation to get
> the molecules as whole or it is a bug.

The "broken" molecules are a consequence of domain decomposition.  So yes, use 
trjconv to correct the frames.  This is not a bug.


> With Regards,
> Gurpreet Singh
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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