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

[Hiromichi Tsurui]

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 [EMAIL PROTECTED]

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