[gmx-developers] polyatomic mutation

Jason DeJoannis jdejoan at emory.edu
Thu Mar 4 20:50:47 CET 2004

Dear gmx-dev,

 I am trying to mutate polyatomic molecules. To start with I am
trying a O2, N2 mixture. The only difference between the molecules
is the LJ parameters and the masses of the atoms. For now I am using
the same bond parameters for both.

 What do I change in order to accomplish the mutation? I am probably 
leaving something out. Right now I change the mass, atom-type, 
atomname, and resname within the 'top->atoms' and 'mdatoms' structures.

 What happens? Well, the single-node run crashes (SIGSEV) during the
neighbor search. I wasn't expecting that. I figured it would crash
during the bonded interactions. By the way, I have had lots of 
success with monatomic mutations (see previous posts). I think I
need to know more about the mystical 'graph' stucture.

 Don't discriminate against mutants! ;)

Jason de Joannis, Ph.D.
Chemistry Department, Emory University
1515 Pierce Dr. NE, Atlanta, GA 30322
Phone: (404) 712-2983
Email: jdejoan at emory.edu

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