[gmx-users] t-couple warning

[JW Feng]

>From reading the wiki, it seems like it is better to couple the entire
system to one thermostat.  Would this better?
tc_grps                 =  system

Thanks,

JW

On 10/11/07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Quoting JW Feng <jw.a.feng at gmail.com>:
>
> > Hello,
> >
> > This is a new warning that appears when executing version 3.3.2 of
> > grompp to create a .tpr file.  Should I be concerned?
> >
> > WARNING 1 [file aminoacids.dat, line 1]:
> >   T-Coupling group PROTEIN has fewer than 10% of the atoms (504 out of
> >   24494)
> >   Maybe you want to try Protein and Non-Protein instead?
> > WARNING 2 [file aminoacids.dat, line 1]:
> >   T-Coupling group CL- has fewer than 10% of the atoms (5 out of 24494)
> >   Maybe you want to try Protein and Non-Protein instead?
> >
> > My mdp options are:
> > ;; TEMPERATURE COUPLING
> > tcoupl                  = berendsen
> > tc_grps                 = PROTEIN  SOL  CL-
> > tau_t                   = 0.1  0.1  0.1
> > ref_t                   = 300 300 300
>
> Don't couple solvent and ions separately.  Merge them into one group with
> make_ndx.
>
> http://wiki.gromacs.org/index.php/Thermostats
>
> -Justin
>
> >
> > Thank you,
> >
> > JW
> >
> > --
> > Jianwen A Feng
> > Center for Computational Biology
> > Washington University in St. Louis
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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://bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ======================
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-- 
Jianwen A Feng
Center for Computational Biology
Washington University in St. Louis