[gmx-users] broken molecules in ouput of MDRUN

Gurpreet Singh gsin at ucalgary.ca
Mon Apr 6 01:39:55 CEST 2009

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

With Regards,
Gurpreet Singh

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