[gmx-users] T-Coupling group
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 25 20:33:05 CEST 2008
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.
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
> 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 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
jalemkul[at]vt.edu | (540) 231-9080
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