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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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