[gmx-users] t-couple warning

[Justin A. Lemkul]

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/

======================