[gmx-users] T-Coupling group

[Serena Leone]

Hello everybody,

I am trying to run a high temperature "rough" dynamic on a polypeptide 
to randomize its structure. When I pre-process the structure in the 
solvent I get the " T-Coupling group XXX has fewer than 10% of the 
atoms" error. This error is also described in the wiki and suggests to 
couple the groups "Protein" and "non-Protein", which I actually did. 
The error message that I get is:


processing index file...
WARNING 1 [file "H1.top", line 998]:
  T-Coupling group Protein has fewer than 10% of the atoms (155 out of
  29508)
  Maybe you want to try Protein and Non-Protein instead?
Making dummy/rest group for Acceleration containing 29508 elements
Making dummy/rest group for Freeze containing 29508 elements
Making dummy/rest group for Energy Mon. containing 29353 elements
Making dummy/rest group for VCM containing 29508 elements
Number of degrees of freedom in T-Coupling group Protein is 464.98
Number of degrees of freedom in T-Coupling group Non-Protein is 58710.02
Making dummy/rest group for User1 containing 29508 elements
Making dummy/rest group for User2 containing 29508 elements
Making dummy/rest group for XTC containing 29508 elements
Making dummy/rest group for Or. Res. Fit containing 29508 elements
Making dummy/rest group for QMMM containing 29508 elements
T-Coupling       has 2 element(s): Protein Non-Protein
Energy Mon.      has 2 element(s): Protein 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...
writing run input file...

but as you can see, the groups are assigned. Beside, line 998 in my 
.top is the line referring to the Cl ions:


993  [ molecules ]
994   ; Compound        #mols
995  Protein_A           1
996  SOL         9782
997  NA+         1
998  CL-         6

but I thought the T-coupling groups were defined in the index file, not 
the topology. Anybody knows what I am doing wrong?

Thanks a lot
Serena

--
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586



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