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
--
========================================
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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