[gmx-users] 1-4 ineractions in double precision

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Jessé Nóbrega wrote:
> 
>>
>> Tcoupl : V-rescale
>>
>> tau_t : 0.1 0.1 0.1
>>
>> tc-grps: protein SOL CL-
>>
>> ref_t : 300 300 300
> 
> The most immediate concern to me (besides trying to alter the 
> table-extension) is here.  Never couple solvent and ions separately.  
> Please see the following:
> 
> http://www.gromacs.org/Documentation/Terminology/Thermostats
> 
> Also, do you get any notes from grompp?  I hadn't seen the use of : in 
> place of = to specify parameters in the .mdp file, and when I tried it, 
> several of my settings (notably tcoupl, pcoupl, and coulombtype) somehow 
> got ignored.  Check your mdout.mdp to make sure you are using the 
> parameters you think you are!

Scratch that; when using ':' to set parameters, *all* of my .mdp options were 
ignored, and set to default values in the .mdp file.  I would say that would be 
a cause for concern :)

-Justin


-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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