[gmx-users] is it any serious error

[Justin A. Lemkul]

Bharath.K. Chakravarthi wrote:
> hello all...
> 
> when ever i run simulation i'm getting this kind of out put saying there 
> is one warning
> as shown below
> 
> 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: 4401 OTHER residues
> There are: 46 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 (460 out of
> 13663)

Have you searched the list archive and Gromacs site for this error?  Certainly 
you would have found this:

http://www.gromacs.org/Documentation/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms

As for whether or not that is appropriate, please read the "Thermostats" entry 
linked from the above page.

-Justin

> Maybe you want to try Protein and Non-Protein instead?
> Making dummy/rest group for Acceleration containing 13663 elements
> Making dummy/rest group for Freeze containing 13663 elements
> Making dummy/rest group for Energy Mon. containing 13663 elements
> Making dummy/rest group for VCM containing 13663 elements
> Number of degrees of freedom in T-Coupling group Protein is 912.90
> Number of degrees of freedom in T-Coupling group Other is 26403.10
> Making dummy/rest group for User1 containing 13663 elements
> Making dummy/rest group for User2 containing 13663 elements
> Making dummy/rest group for XTC containing 13663 elements
> Making dummy/rest group for Or. Res. Fit containing 13663 elements
> Making dummy/rest group for QMMM containing 13663 elements
> T-Coupling has 2 element(s): Protein Other
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 44x44x44, spacing 0.118 0.118 0.118
> writing run input file...
> 
> There was 1 warning
> 
> gcq#100: "Proceed, With Fingers Crossed" (TeX)
> 
> 
> 
> -- 
> Bharath.K.Chakravarthi
> Ph:9535629260
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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