[gmx-users] mdrun error during pr

[Tsjerk Wassenaar]

Hi Dhananjay,

Happy new year :)

Just what it says: not enough ref_t and tau_t values. You use
"Protein" and "Sol" as temperature coupling groups, but likely, you
also have ions in your system, which are not coupled now. You may want
to use "Protein" and "Non-Protein" in stead. In case you have some non
standard groups (modified amino acid, ligands, cofactors), you need to
use an index group. Do not think of giving a cofactor/ligand/small
group of ions a private heat bath. Check the archives using "Not
enough ref_t and tau_t values" as search string, or simply ref_t and
tau_t. You should've done that before posting, really, because this
issue has been dealt with several times already, including
explanations of why not giving private heat baths.

Cheers,

Tsjerk


On 1/2/07, Dhananjay <dhananjay.c.joshi at gmail.com> wrote:
> Hello all,
>
> I have minimized the pdb file and wish to do mdrun for position restrain
> dynamics.
> For this when I run grompp programm, it is showing error as follows. I don't
> understand why it is showing this error:
>
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> Reading position restraint coords from 2HT1_b4pr.gro
> renumbering atomtypes...
> converting bonded parameters...
> #  G96ANGLES:   9382
> #      PDIHS:   3544
> #      IDIHS:   2984
> #       LJ14:   10898
> #     POSRES:   5054
> #     CONSTR:   6472
> #     SETTLE:   25639
> Walking down the molecule graph to make shake-blocks
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
> /users/soft/GromacsSingle/share/gromacs/top/aminoacids.dat
> There are: 25641      OTHER residues
> There are:   648    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 10 elements
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: readir.c, line: 1131
>
> Fatal error:
> Not enough ref_t and tau_t values!
> -------------------------------------------------------
>
> "I was detained, I was restrained" (The Smiths)
>
>
>
> Please anybody tell me what is wrong here ?
> for the reference I have attached pr.mdp file
>
> Thanking you in advance......
>
>
> -- Dhananjay
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623