<div>hello all...<br clear="all"></div><div><br></div><div>when ever i run simulation i'm getting this kind of out put saying there is one warning</div><div>as shown below</div><div><br></div><font face="courier new,monospace">Walking down the molecule graph to make shake-blocks<br>
initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>There are: 4401 OTHER residues<br>There are: 46 PROTEIN residues<br>
There are: 0 DNA residues<br>Analysing Protein...<br>Analysing Other...<br>WARNING 1 [file aminoacids.dat, line 1]:<br> T-Coupling group protein has fewer than 10% of the atoms (460 out of<br> 13663)<br> Maybe you want to try Protein and Non-Protein instead?<br>
Making dummy/rest group for Acceleration containing 13663 elements<br>Making dummy/rest group for Freeze containing 13663 elements<br>Making dummy/rest group for Energy Mon. containing 13663 elements<br>Making dummy/rest group for VCM containing 13663 elements<br>
Number of degrees of freedom in T-Coupling group Protein is 912.90<br>Number of degrees of freedom in T-Coupling group Other is 26403.10<br>Making dummy/rest group for User1 containing 13663 elements<br>Making dummy/rest group for User2 containing 13663 elements<br>
Making dummy/rest group for XTC containing 13663 elements<br>Making dummy/rest group for Or. Res. Fit containing 13663 elements<br>Making dummy/rest group for QMMM containing 13663 elements<br>T-Coupling has 2 element(s): Protein Other<br>
Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>
XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>Calculating fourier grid dimensions for X Y Z<br>
Using a fourier grid of 44x44x44, spacing 0.118 0.118 0.118<br>writing run input file...<br><br>There was 1 warning<br><br>gcq#100: "Proceed, With Fingers Crossed" (TeX)</font><br><br><br><br>-- <br>Bharath.K.Chakravarthi<br>
Ph:9535629260<br>