[gmx-users] Fatal error: Not enough ref_t and tau_t values!

[David van der Spoel]

On Tue, 2005-02-01 at 11:13 +0200, Markus O Kaukonen wrote:
> Dear All,
> 
> My system is a protein embedded in tip4 water.
> oplsaa force field is used.
> Trying to mdrun it at NPT.
> 
> Question:
> When running grompp one gets output:
> >Setting particle type to Dummy for dummy atoms
> >Walking down the molecule graph to make shake-blocks
> >initialising group options...
> >processing index file...
> >Making dummy/rest group for T-Coupling containing 22354 elements
> >Fatal error: Not enough ref_t and tau_t values!
> 
> So it seems to me that grompp generates new temperature group
> (for dummy atoms of tip4 water?)
> but cannot find ref_t and tau_t values.
> 
> Tried adding more ref_t and tau_t values in .mdp file but that also causes
> fatal error.
> 
> Is there a way around?
are you giving it an incorrect index file? without index file it should
just generate one group for the whole system.
running a protein in water with just one temperature coupling group may
not be a good idea by the way.
> My .mdp file is below
> 
> Terveisin Markus
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl                   = berendsen
> ; Groups to couple separately =
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 0.1
> ref_t                    = 300
> ; Pressure coupling      =
> Pcoupl                   = berendsen
> Pcoupltype               = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = no
> gen_temp                 = 340.0
> gen_seed                 = 173529
> 
> cpp                 =  /lib/cpp
> define              =
> integrator          =  md
> nsteps              =  500000
> dt                  =  0.001
> 
> 
> 
> 
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout                  = 10000
> nstvout                  = 100000
> nstfout                  = 100000
> 
> ; Output frequency for energies to log file and energy file
> nstlog                   = 1000
> nstenergy                = 1000
> 
> pbc                      = xyz
> 
> ns_type                  = grid
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> vdwtype = Shift
> rlist=1.0
> rvdw=0.9
> rvdw_switch=0.8
> rcoulomb = 0.9
> fourierspacing           = 0.075
> pme_order                = 4
> ewald_rtol               = 1e-05
> optimize_fft             = yes
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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