[gmx-users] ref_tau error message

[Marian Zlomislic]

Hi Maria,
Index files are specific to the system that you're studying.

you can use:

make_ndx -f x.gro -o index.ndx 

where x.gro is the name of your structure file to generate your own.
Run this command, and then look at your index.ndx file, and you'll see that 
by default, all of the atoms have been listed in categories such as [System], 
[Protein], etc.

once you've done this, you'll see that the default groups that are generated 
all have numbers and names.  To generate a SOL_Cl group (that includes all of 
the atoms in the solvent and the cl ions) you can use:

" <insert group number for SOL> | <insert group number for Cl>  "

In my case, it was:
13 | 14

I hope that helps.
marian



Maria Sabaye Moghaddam <msabaye at gibbs.med.utoronto.ca> said:

> 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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