[gmx-users] t-couple warning

[Mark Abraham]

Justin A. Lemkul 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.

Or like the warning suggests, use the default Non-Protein group in the 
(auto-created) index groups.

> http://wiki.gromacs.org/index.php/Thermostats
> 
> -Justin

Mark