[gmx-users] from molecule to radical

Li Xiaoyi xiaoyi.li at nat.oru.se
Wed Apr 14 16:47:01 CEST 2004

Dear all,

Is the following progress the right and completed way to put radical
into MD simulation by Gromacs?
1, Get the .top file of the corresponding molecule by PRODRG.
2, Delete the hydrogen atom of this molecule in the top file.
3, Change the partial charge in the top file under "[ atoms ], charge"
using the result of QM calculations.

I read in the mailing-list that it's not proper to change the partial
charge using the result of QM calculations. Is there any other methods
to adjust the partial charge to fit the Gromacs?

Anothe question: what's the meaning of cgnr in the top file?


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