[gmx-users] ref_tau error message

[Maria Sabaye Moghaddam]

Hi Marian;

    If it is not too much to ask, can I have a copy of your index file to 
use as a template?  I cannot find a sample index file anywhere.  

Thanks a lot,
Maria.


On Tue, 21 Sep 2004, Marian Zlomislic wrote:

> Hi Maria,
> In your .mdp file, how many different tc-grps have you specified?  For 
> example, in my simulation of a peptide in octane, in water with ions, i have 
> three tc-groups:
> tc-grps     Protein  OCT   SOL_Cl
> and so i also have 3 tau_t and ref_t groups:
> tau_t   0.1   0.1   0.1
> ref_t   300   300   300
> 
> These grps are defined by the list of atom numbers following each name (ie. 
> [Protein], [OCT], and [SOL_Cl]) in my index file.
> 
> i hope that was helpful.
> mz
>  
> 
> Maria Sabaye Moghaddam <msabaye at gibbs.med.utoronto.ca> said:
> 
> > Thanks Xavier, but I don't know what that means.  That is I don't know
> > where to look for this problem or how
> > to fix it. I am very new with gromacs and I am following the steps 
> > by reading the manual and the Getting Started.  I don't see much detail 
> > about any of these there.  Can anyone help me with this?
> > 
> > Best,
> > Maria.
> > 
> > 
> > >
> > >I am getting:
> > >....
> > >....
> > >Making dummy/rest group for T-Coupling containing 2 elements
> > >Fatal error: Not enough ref_t and tau_t values!
> > >
> > >changing the ref_t and tau_t values in name.mdp doesn't change the 
> > >outcome.  Does anyone know what I should do?
> > >
> > That is probably because you have atoms not included in the different subset
> > of atoms (group of atoms) included in the different baths of temperature.
> > 
> > XAvier
> > 
> > -- 
> > ----------------------------------------------
> > 
> >    Xavier Periole - Ph.D.
> > 
> >    Dept. of Biophysical Chemistry / MD Group 
> >    Univ. of Groningen
> >    Nijenborgh 4
> >    9747 AG Groningen
> >    The Netherlands
> > 
> >    Tel: +31-503634329
> >    Fax: +31-503634800
> >    email: x.periole at chem.rug.nl
> >    web-page: http://md.chem.rug.nl/~periole
> >    
> > ----------------------------------------------
> > 
> > 
> > ----- End forwarded message -----
> > 
> > 
> > 
> > 
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> 
> -- 
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