[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.
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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