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

[Yang Ye]

On 10/18/2006 8:10 AM, Aline Rossi wrote:
> Hi list,
>
> Im dealing with a problem when trying to monitoring energygrps. When I
> run the grompp i receive this output:
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> Excluding 3 bonded neighbours for Protein_C 1
> Excluding 2 bonded neighbours for SOL 30314
> Excluding 1 bonded neighbours for NA+ 2
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 312 K
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   6825
> #  G96ANGLES:   9964
> #      PDIHS:   3583
> #      IDIHS:   3430
> #       LJ14:   10944
> #     SETTLE:   30314
> initialising group options...
> processing index file...
> Making dummy/rest group for T-Coupling containing 90944 elements
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: readir.c, line: 1131
>
> Fatal error:
> Not enough ref_t and tau_t values!
>
> my index file is:
> 0 System              : 96772 atoms
>  1 Protein             :  6694 atoms
>  2 Protein-H           :  5213 atoms
>  3 C-alpha             :   666 atoms
>  4 Backbone            :  1998 atoms
>  5 MainChain           :  2667 atoms
>  6 MainChain+Cb        :  3268 atoms
>  7 MainChain+H         :  3306 atoms
>  8 SideChain           :  3388 atoms
>  9 SideChain-H         :  2546 atoms
> 10 Prot-Masses         :  6694 atoms
> 11 Non-Protein         : 90078 atoms
> 12 Mg                  :     7 atoms
> 13 SOL                 : 90069 atoms
> 14 NA+                 :     2 atoms
> 15 Other               : 90078 atoms
> 16 alpha&beta          :  6648 atoms
> 17 his159              :    12 atoms
> 18 arg157              :    17 atoms
> 19 ecdw                :    51 atoms
> 20 glu1                :    12 atoms
> 21 cys2                :     8 atoms
> 22 asp3                :     9 atoms
> 23 trp4                :    22 atoms
> 24 tyr458              :    18 atoms
> 25 ala585              :     6 atoms
> 26 prot+pep            :  6703 atoms
> 27 prot+pep+mg         :  6706 atoms
> 28 alpha               :  4453 atoms
> 29 beta                :  2202 atoms
> 30 pep                 :    51 atoms
> title               =  PEP MD
> cpp                 =  /lib/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.0015    ; ps !
> nsteps              =  10000000    ; total 500 ps.
> nstcomm             =  3000
> nstxout             =  3000
> nstvout             =  5000
> nstfout             =  3000
> nstlog              =  1500
> nstenergy           =  3000
> nstlist             =  5
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing          =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> unconstrained-start      = yes
>
> ; Berendsen temperature coupling is off in two groups
> Tcoupl              =  berendsen
> tc-grps            =  alpha     beta      pep
> tau_t               =  0.1       0.1       0.1
> ref_t               =  312       312       312
> ; Energy monitoring
> energygrps          =  alpha    beta    pep
beside the proteins, solvent also needs t-coupl.
Try this
tc-grps            =  alpha     beta      pep  rest
tau_t               =  0.1       0.1       0.1    0.1
ref_t               =  312       312       312  312
; Energy monitoring
energygrps          =  alpha    beta    pep rest
>
> ; Isotropic pressure coupling is  on
> Pcoupl              =  berendsen
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
>
> ; Generate velocites is on at 312 K.
> gen_vel             =  yes
> gen_temp            =  312.0
> gen_seed            =  173529
>
> What should be wrong with my imputs??
>
>
>
> Thanks for help
> and my .mdp file is:
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