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

[Tsjerk Wassenaar]

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,

Tsjerk

On 2/14/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> David Mathog wrote:
> > Tamas Horvath wrote:
> >
> >> Check out what groups you have. The values at tau_t and ref_t refer to
> >>
> > those
> >
> >> groups.
> >> In the default case, in the demo, those refer to "protein" and "SOL"
> >>
> > groups.
> >
> > I went another way on this one.  Since the values in each column
> > are the same (at least in the demos) I modified readir.c so that it
> > just filled in the missing tau_t and ref_t values with those from
> > the last column.  After emitting a warning of course.  Then it ran
> > to completion.
> >
> Sounds like a useful hack, since it is quite rare that one used
> different values. Can you send me the hacked readir.c code?
> A general problem with automating stuff is that people may stop
> thinking... Let's be honest if you want to get something done and get a
> messagebox with the options Cancel OK, then you click OK (I do...).
> However for scientific programs the user should know what (s)he's doing...
> > Which brings up the next mystery.  When ngmx runs on the output
> > the filter screen has
> >
> > Group-1: system,protein,protein-h,c-alpha,backbone,
> > mainchain,mainchain_Cb, and MainChain+H
> > Group-2: sidechain,sidechain-H,prot-masses,nonprotein,CA,SOL,Other
> >
> > In the gmxdemo with cpeptide there was only one Group-1, which
> > contained all of the entries from Groups 1 and 2 except CA.
> >
> > What significance does one group vs. two have?  Any?  Is it just that
> > the program thinks the menu is too long and splits it at 15 entries?
> >
> It's just that, they won't fit on the screen otherwise.
>
>
> If you have more hacks that you think are of general interest please
> send them to me.
> Thanks,
>
> --
> 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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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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