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

[Yang Ye]

Does your index.ndx has all the atom numbers?

Yang Ye

Miguel Ortiz Lombardia wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi all,
>
> I get this error from grompp:
>
> Program grompp, VERSION 3.3
> Source code file: readir.c, line: 1131
>
> Fatal error:
> Not enough ref_t and tau_t values!
>
> However, I do have three values for ref_t and tau_t, as many as groups
> (I made an index.ndx file that I feed to grompp to support the
> non-standard group ('Na')
>
> This is my input:
>
>
> title                    = 20ps Position-restrained MD
> cpp                      = /lib/cpp -traditional
> define                   = -DPOSREF
> integrator               = md
> dt                       = 0.002
> nsteps                   = 10000
> nstxout                  = 1000
> nstvout                  = 1000
> nstlog                   = 1000
> nstenergy                = 50
> nstxtcout                = 50
> xtc_grps                 = Protein
> energygrps               = Protein  SOL  Na
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 0.9
> coulombtype              = PME
> rcoulomb                 = 0.9
> rvdw                     = 0.9
> tcoupl                   = Berendsen
> tc-grps                  = Protein  SOL  Na
> tau_t                    = 0.1  0.1  0.1
> ref_t                    = 300  300  300
> Pcoupl                   = Berendsen
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> constraints              = all-bonds
>
>
> Any clues?
>
>
> Cheers,
>
>
> Miguel
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> email: molatwork at yahoo.es
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Je suis de la mauvaise herbe,
> Braves gens, braves gens,
> Je pousse en liberté
> Dans les jardins mal fréquentés!
>                                                        Georges Brassens
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.1 (GNU/Linux)
>
> iD8DBQFEDXRaF6oOrDvhbQIRAhByAJ40oJ5y86tdQPbFeMutns0yBqkCFACfaKwJ
> 37v80Jrxt3Vwsj2hHYilG4k=
> =KzZb
> -----END PGP SIGNATURE-----
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>