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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 18 10:21:59 CEST 2006


Hi Aline,

Maybe a word of warning is in place. It is probably not a good idea to
couple different parts of the same protein to different heat baths. It
is definitely not a good idea to couple one peptide of 51 atoms to its
private bath. You are likely better off with the division Protein
Non-Protein (two tc-groups). This stands apart from the energy groups,
where you can make the division alpha/beta/pept. Noting that you do
have some magnesium ions, it may be necessary to have these in one
index group, which you have actually, and for the solvent just make
the complementary index group by merging the groups SOL and NA+ (or
negating prot+pep+mg.

Hope it helps,

Tsjerk

On 10/18/06, Yang Ye <leafyoung81-group at yahoo.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
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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