[gmx-users] Re:gmxdemo: peptide to real protein and boom

[David van der Spoel]

Tsjerk Wassenaar wrote:
> Hi David,
> 
> Though I see some sense in having the proposed hack, it should be used 
> with care since in most cases the additional groups will be ions or 
> small subsets of atoms, which are better not to be coupled to a heat 
> bath independently. I would advocate not to rely on such an option, but 
> rather check the pdb for non-standard groups or use the 
> protein/non-protein groups.
> 
> JM2C,
> 
I agree, but you can do both as well. If you take care to have the 
distinction Protein/Non-Protein in your Tcoupl groups then coupling will 
be fine. However for Energy groups you'd rather have Protein Sol Ions as 
a default (at least I do).

If there are proper (and understandable) warnings we've done what we can 
to illuminate the user. Isn't that enough?


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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