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

Justin Lemkul jalemkul at vt.edu
Tue Sep 25 23:47:42 CEST 2012

On 9/25/12 5:42 PM, Andrew DeYoung wrote:
> Hi,
> 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?

It would be 1.

> (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.

It does nothing.

>>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

Correct (given the caveats you list above), so at the very least, syntactically 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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