[gmx-users] addition of the .itp file of a new residue

soumadwip ghosh soumadwipghosh at gmail.com
Fri Nov 21 05:16:09 CET 2014

Thanks justin for your help. Just one question. The .itp file I made by
using ParamChem and your university server, gave me the total charge for
tetramethyl ammonium molecule + 1.1 (shown by qtot) while it should be 1
actually. My system contained -22 negative charge and for my work I just
need to neutralize the system. So, I added 20 tma via ci and nmol option.
Now everything is going fine with the simulation but my question is can the
+1.1 charge of discreet tma species hamper or overestimate the real
dynamics and the interaction of DNA with the ions present.

Thanks and regards,

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