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

[Miguel Ortiz Lombardia]

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Hi and thank you for your answer,

Unfortunately, it didn't help.

I'm wondering if the reason is that the structure file from which I do
the index and would like to use for the md is in 'pdb' format. This
structure file comes from a previous mdrun where I performed an energy
minimization. To test this hypothesis I converted this structure file to
'gro' format using editconf, simply:

editconf -f after_em.pdb -o after_em.gro

and then tried to make the index file again from the latter file. It
didn't work either. But I thought the problem might be in the 'pdb'
structure file produced by mdrun.

Could this happen?

Cheers,


Miguel

MGiò wrote:
> Hi Miguel!
> the same thing happened to me just yesterday. My problem was that, for
> some reasons not worth to tell, some atoms were missing from one of my
> groups. I made a new index.ndx file and no errors were reported anymore.
> So my piece of advice is check your index file. I hope it helps,
> greetings,
> MGiò
> 
> 
> On 3/7/06, *Miguel Ortiz Lombardia* <molatwork at yahoo.es
> <mailto:molatwork at yahoo.es>> wrote:
> 
> 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 <mailto: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
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- --
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
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