[gmx-users] tcoupling

[Justin A. Lemkul]

Mark Abraham wrote:
> 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?

Or one less :)

-Justin

> 
>> 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
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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