[gmx-users] T-Coupling group

[Justin A. Lemkul]

What's happening is that grompp is reaching the end of your topology 
(line 998) and identifying what it thinks is a problem.  I'm guessing 
your peptide has 155 atoms?  Using Protein Non-protein is fine, and is 
the best thing to do in this scenario.  The warning is really meant to 
alert individuals who do something like:

tc-grps = Protein SOL NA+ CL-

which is destined for problems.

I'd say everything you've done is fine.

-Justin

Serena Leone wrote:
>
> 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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-- 
========================================

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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