[gmx-users] Final structure broken

[Justin Lemkul]

On 5/14/18 8:52 PM, Dhumal, Nilesh wrote:
> Just for curiosity, Why it is not broken at 400 K? I didn't see similar results for other system also. I did simulation for 800 water molecules using same mdp file, the final structure was not broken.

Maybe every atom just happened to be within the box. Regardless, always 
apply trjconv in the proper sequence and you'll never have problems in 
any system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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