[gmx-users] Error: Not enough ref_t and tau_t values

[Tsjerk Wassenaar]

Hi Hiromichi,

It is likely that you have some groups which are not covered by "Protein"
and "Other". You can use "Protein" and "Non-Protein" in stead. But make sure
that the two groups correspond to two distinct groups in your system. You
may run into trouble if you have some non-standard residue in your protein
which will end up in the "Non-Protein" group.

Cheers,

Tsjerk

On 6/14/06, Hiromichi Tsurui <tsurui at med.juntendo.ac.jp> wrote:
>
>  Dear all;
>
>
>
> I am trying to calculate the binding free energy of an MHC-molecule and a
> peptide by thermodynamic integration method. The system contains binding
> domain of MHC molecule, a peptide presented on it, water-molecules (about
> 13,000), and ions (Na+ and Cl- at PBS-concentration).
>
> After energy minimization, I tried to equilibrate the system with the
> mdp-file as follows, and an error-message appeared as such;
>
> "Fatal error.
>
> Not enough ref_t and tau_t values."
>
> How should I change the conditions ?
>
>
>
> Many thanks for your help.
>
>
>
>
>
> cpp                 =  /lib/cpp
> define              =
> integrator          =  md
> tinit               =  0.0
> dt                  =  0.002
> nsteps              =  100000
> nstcomm             =  1
> nstxout             =  50000
> nstvout             =  50000
> nstfout             =  0
> nstlog              =  10000
> nstenergy           =  250
> nstxtcout           =  10000
> xtc_precision       =  1000
> xtc_grps            =  Protein
> energygrps          =  Protein other
> nstlist             =  5
> ns_type             =  grid
> pbc                 =  xyz
> rlist               =  0.9
> coulombtype         =  Reaction-Field
> epsilon_r           =  78.0
> rcoulomb            =  1.4
> vdw-type            =  Cut-off
> rvdw                =  1.4
> tcoupl              =  Berendsen
> tc-grps             =  Protein other
> ref_t               =  300 300
> tau_t               =  0.1 0.1
> pcoupl              =  Berendsen
> tau_p               =  1.0
> compressibility     =  4.6e-5
> ref_p               =  1.0
> gen-vel             =  yes
> gen-temp            =  300
> gen-seed            =  $RANDOM
> constraints         =  all-bonds
>
> Hiromichi Tsurui MD, PhD
> Dept. Pathology,
> Juntendo University
> Phone:81-3-5802-1039
> Fax:81-3-3813-3164
> tsurui at med.juntendo.ac.jp
>
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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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