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

[Florian Haberl]

hi

On Tuesday 07 March 2006 12:54, Miguel Ortiz Lombardia 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?

can you please post the last lines of your top file :

Could look like

[ molecules ]
; Compound        #mols
Protein          1
SOL              8502
Na                  4

so here you need 3 t-* values or you can do something like:

[in your mdp]

tc-grps =      protein non-protein

so only two values.

other thing is: perhaps you have taken the wrong .top file so top and gro file 
are not the correct onces.
>
>
> Cheers,
>
>
> Miguel

greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------