[gmx-users] tcoupling

[Mark Abraham]

shahrbanoo karbalaee wrote:
> hi justin
> I have a file  tfe  peptide water,cl  .I  minimized it and I  want to
> preequilbrate it.when I do the grompp  I get  1 warning:
>  calling /lib/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> turning all bonds into constraints...
> Excluding 3 bonded neighbours for TFE 200
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 913
> turning all bonds into constraints...
> Excluding 1 bonded neighbours for CL- 1
> turning all bonds into constraints...
> NOTE:
>   System has non-zero total charge: -1.000003e+00

Perhaps you want another chloride ion?

> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> Reading position restraint coords from emout.gro
> renumbering atomtypes...
> converting bonded parameters...
> #  G96ANGLES:   1803
> #      PDIHS:   468
> #      IDIHS:   68
> #       LJ14:   1010
> #     POSRES:   105
> #     CONSTR:   1339
> #     SETTLE:   913
> Walking down the molecule graph to make shake-blocks
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are:  1114      OTHER residues
> There are:    14    PROTEIN residues
> There are:     0        DNA residues
> Analysing Protein...
> Analysing Other...
> WARNING 1 [file aminoacids.dat, line 1]:
>   T-Coupling group Protein has fewer than 10% of the atoms (138 out of
>   4278)
>   Maybe you want to try Protein and Non-Protein instead?

> ; Berendsen temperature coupling is on
> Tcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_t               =  0.1         0.1
> tc-grps             =  Protein    non-protein
> ref_t               =  300        300

I think this is probably an issue with case-sensitivity. The warning 
exists to help people avoid erroneously coupling a handful of ions to 
their own thermostat. Your system is probably fine with the two kinds of 
groups you have. You could just ignore the warning, or edit your .mdp 
file (and/or index file) to capitalize to "Non-Protein"

Mark