[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
tsurui at med.juntendo.ac.jp 
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