[gmx-users] Deuterate, heavyh options inconsistent

[Justin Lemkul]

On 7/27/12 9:55 PM, Ladasky wrote:
> Hello Mark,
>
> Thanks for your reply.  It has taken me several days to make some progress
> on my issues.  I'm just going to address one specific point in this post.
>
>
> Mark Abraham wrote
>>
>> On 19/07/2012 6:52 PM, Ladasky wrote:
>>
>>> I once used the -deuterate option in pdb2gmx, and I am presently trying
>>> to avoid it.  I asked whether -deuterate has any effect on water
>>> molecules
>>> in a previous post, or only on the hydrogens in proteins.  So far, I have
>>> not been made to understand that genbox silently deuterates water
>>> hydrogens,
>>> if it receives a deuterated protein as input.
>>
>> Probably. You'd have to inspect the atom types in the resulting
>> processed topology (e.g. from grompp -pp) to be sure.
>>
>
> I have now had a chance to look at this issue.  I generated a small,
> tri-peptide protein, and solvated it in a small box of solvent. I tried
> pdb2gmx once in default mode for hydrogen atoms, once with the -deuterate
> option, and once with the -heavyh option.  I looked at the topology files
> produced by grompp -pp.
>
> Excerpt of grompp_1.top (pdb2gmx default, normal hydrogen):
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
> ; residue   1 ALA rtp ALA  q +1.0
>       1         NL      1    ALA      N      1      0.129    14.0067   ; qtot
> 0.129
>       2          H      1    ALA     H1      1      0.248      1.008   ; qtot
> 0.377
>
> (snip)
>
> ; Include water topology
> [ moleculetype ]
> ; molname	nrexcl
> SOL		2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>       1     OW      1    SOL     OW      1      -0.82   15.99940
>       2      H      1    SOL    HW1      1       0.41    1.00800
>       3      H      1    SOL    HW2      1       0.41    1.00800
>
> Here are the same parts of grompp2.top, generated using the -deuterate
> option in pdb2gmx.  Protein hydrogens have increased mass.  Solvent
> hydrogens DO NOT have increased mass.  Heavy atoms to which deuterated
> hydrogens have been attached do not have reduced mass.
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
> ; residue   1 ALA rtp ALA  q +1.0
>       1         NL      1    ALA      N      1      0.129    14.0067   ; qtot
> 0.129
>       2          H      1    ALA     H1      1      0.248      2.016   ; qtot
> 0.377
>
> ; Include water topology
> [ moleculetype ]
> ; molname	nrexcl
> SOL		2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>       1     OW      1    SOL     OW      1      -0.82   15.99940
>       2      H      1    SOL    HW1      1       0.41    1.00800
>       3      H      1    SOL    HW2      1       0.41    1.00800
>
> Finally, here the same parts of grompp4.top (pdb2gmx -heavyh option).  This
> time, solvent hydrogens ARE given an increased atomic weight, and the
> solvent oxygen is reduced in atomic weight to make up the difference.  In
> the protein, the mass of the heavy atom to which hydrogens attach is also
> reduced.
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
> ; residue   1 ALA rtp ALA  q +1.0
>       1         NL      1    ALA      N      1      0.129     4.9347   ; qtot
> 0.129
>       2          H      1    ALA     H1      1      0.248      4.032   ; qtot
> 0.377
>
> ; Include water topology
> [ moleculetype ]
> ; molname	nrexcl
> SOL		2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>       1     OW      1    SOL     OW      1      -0.82    9.95140
>       2      H      1    SOL    HW1      1       0.41    4.03200
>       3      H      1    SOL    HW2      1       0.41    4.03200
>
>
> This was in fact the concern that occurred to me when I abandoned the use of
> -deuterate.  I wondered about the consequences of changing the atomic weight
> of hydrogen.  I wondered further about the unrealistic nature of a
> heterogenous system, with some normal-mass hydrogens and some heavy
> hydrogens.  As I did not see any option for adjusting the solvent hydrogen
> mass, I assumed that the system would be mixed, and I was right.
>
> It was stranger still to see that the -heavyh option, which I've never used,
> DOES alter solvent hydrogen masses, to make a uniform system.
>
> Are these two distinct behaviors what GROMACS users want?  Or did I just
> uncover a bug?
>

These are distinct behaviors by design.  The use of heavy hydrogens (4x mass) is 
used in cases where one might want to increase the time step.  This is described 
in the last paragraph of the pdb2gmx help info.  Deuteration is carried out on 
the solute with which pdb2gmx is presented; if one wants to model D2O, one needs 
a suitable parameter set for it.  I suspect it exists somewhere, but have never 
had a need to go looking for one myself.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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