[gmx-users] Not enough ref_t and tau_t values

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 16 10:09:32 CET 2006

Hi Ashutosh,

If no index file is explicitly given to grompp, it will use default index
group (as if you did echo q | make_ndx -f test_b4pr.gro -o index.ndx) Grompp
does not know of definitions given in the .top file with regards to the
groups. Does your protein contain some non-standard residues? Try to
explicitly create an index file and see if the groups "Protein" and "SOL"
cover all atoms in your system. ( N(Proteins) + N(SOL) = N(System) ). If
not, make adjustments to the index file by merging appropriate groups, i.e.
merge non-standard protein groups with the protein if necessary. Note that
this basically was the problem given in the last post about "Not enough
ref_t and tau_t values".



On 3/16/06, X.Periole <X.Periole at rug.nl> wrote:
> On Wed, 15 Mar 2006 17:21:52 -0600
>   Ashutosh Jogalekar <ajogale at emory.edu> wrote:
> > I know this question has been discussed a number of
> >times on the  list, but almost everytime it has been
> >discussed in reference to the  index file.
> > I am getting this error during grompp for the position
> >restrained MD  even though I am not using any index file.
> >The only groups I have are  solvent and protein and
> >accordingly, there are two columns for these  two in the
> >tau_t and ref_t fields in the pr.mdp file:
> >
> > tau_t=       0.1         0.1
> > tc_grps=   protein  sol
> > ref_t=        300       300
> >
> > my command is:
> >
> > grompp -f pr.mdp -c test_b4pr.gro -p test.top -o
> >test_em.tpr
> >
> > In spite of this, the error is showing up again and
> >again. The top  file also has a row only for protein and
> >solvent.
> If all the atoms of your protein or solvent are not
> included
> in the indexes defined by default (protein sol) I think
> grompp find them out of any index and then looks for more
> tau_t and ref_t ... I would check the topology of your
> system. It might be uncorrect.
> XAvier
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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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