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

[David van der Spoel]

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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