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

Berk Hess gmx3 at hotmail.com
Wed Feb 15 17:01:35 CET 2006

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Re:gmxdemo: peptide to real protein and boom
>Date: Wed, 15 Feb 2006 10:55:16 +0100
>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 
>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?

I have another reason for not implementing such a hack.
When you use an (edited) index file, you might forget
one or two atoms, for which grompp automatically makes
a rest group and then makes a tpr file.
Most people do not read the warnings and would just run the simulations.

We could copy the t-coupling values, but then grompp should
not automatically make rest groups.

Now I think of it, we should anyhow only generate the rest groups for
cases where nothing happens to them (such as xtc and freeze groups)
and generate a fatal error in all other cases.


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