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

[Hiromichi Tsurui]

Thank you Tsjerk;

I followed your advice, and it looks working well.

Cheers,

Hiromichi
  ----- Original Message ----- 
  From: Tsjerk Wassenaar
  To: Discussion list for GROMACS users
  Sent: Wednesday, June 14, 2006 8:13 PM
  Subject: Re: [gmx-users] Error: Not enough ref_t and tau_t values


  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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