[gmx-users] tcoupling

[Tsjerk Wassenaar]

Hi,

I haven't really checked how it is with the new version (and you're
not telling which version you're using anyway), but grompp used to get
confused with multiple molecules and only report the charge on one of
them. You can check the total charge from the .tpr file with (bash
command line):

gmxdump -s topol.tpr 2>/dev/null | grep "atom\[" | awk -F, '{print
$5}' | awk -F= '{sum+=$2}END{print int(sum+0.499)}'

Cheers,

Tsjerk

On Sun, Oct 26, 2008 at 12:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>
> --
> ========================================
>
> 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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-- 
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