[gmx-users] NOE restraints and undefined hydrogen atoms, virtual interaction sites

Louic Vermeer louic at louic.nl
Thu Jan 31 11:26:11 CET 2008

On Wednesday 30 January 2008 23:56, Mark Abraham wrote:

> There's no a priori reason why a mixture of a united-atom detergent
> sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither
> is there any reason to suppose they *would* work without evidence that
> the SDS parameters were developed with this purpose in mind and suitably
> validated. For that, you'll have to read the paper referred to on the
> page you footnoted [1], I guess.

Obviously, I read the paper that I referred to in my question. The authors 
have simulated SDS in water at different concentrations, using a united atom 
"gromacs" forcefield (they don't mention the forcefield more precisely in the 
paper or in the topology file itself). They do not mention that the SDS was 
designed for other reasons than simulations of SDS itself. The validation of 
the SDS topology file was done by the authors of the paper, to me it seems 

Several messages on this list have pointed out that mixing forcefields is not 
a good idea. To use united-atom SDS with an all-atom peptide, it seems to me 
that I would have to mix two forcefields. I would prefer to use a united atom 
forcefield for both the SDS and the peptide. Which leaves open my question 
about the definition of NOE restraints (on protons) when using a united-atom 

> Your other alternative is looking for 
> an all-atom SDS topology that has been validated, but I've no idea
> whether one exists.

It does not seem to exist. To the best of my knowledge the paper cited in my 
initial question is the first and only publication of a gromacs simulation of 
SDS. Even if it did exist, I am more interested in the united-atom approach 
because the simulation I plan to do will be a long one (long computation 

> Regarding your footnote [2], you've provided a link to the mailing list
> search page on the GROMACS webpage, which contains multiple frames. The
> link you actually need to provide is the one to the frame that had the
> email to which you wish to refer.

This is the link I intended to include. It leads to an answer by Anton 
Feenstra to a question on a related subject.

> Mark

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