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

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 15 10:55:16 CET 2006

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 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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