[gmx-users] Deuterium and the meaning of the atomic number parameter

Andrew DeYoung adeyoung at andrew.cmu.edu
Tue Sep 25 23:42:25 CEST 2012


In my system, I have several hydroxyl groups.  I would like to change the
hydroxyl hydrogens to deuterium (as an approximation, I will just double the
typical hydrogen mass).  I am only doing this as a test of the dependance on
mass of my system, so while I am sure force fields involving deuterium exist
in the literature, I will not be using them. 

My question is, if I am simply doubling the mass of my hydroxyl hydrogens,
what atomic number should I use in my ffnonbonded.itp file?  1 or 2?  

(Since the mass of each atom is always specified in the topology, it is not
clear to me what the atomic number parameter does in Gromacs.)

Section 5.3.2 of the manual shows how the atomic number ("at.num" in the [
atomtypes ] directive) is specified in ffnonbonded.itp, but it is not clear
to me what the atomic number actually does in Gromacs.

>From general chemistry, I know that the atomic number is simply the number
of protons in the nucleus.  Deuterium's nucleus consists of one proton and
one neutron, so the atomic number of deuterium should be 1.  

Am I correct in setting the atomic number of deuterium as 1?  Then my
ffnonbonded.itp file will look like:

[ atomtypes ]
;name   at.num   mass            charge         ptype   sigma  epsilon
 HO      1       2.01580         0.418          A   ; sigma, epsilon

Thank you for your time!

Andrew DeYoung
Carnegie Mellon University

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