[gmx-users] T-coupling problem?

[Justin A. Lemkul]

Talal Alotaibi wrote:
> Hi,
>  
> I am trying to freeze the protein during equilibruim. I made the energy 
> minimization with no freezing. but when I freeze the protein and try to 
> do "grompp", it gives me this error:
> ==============================================
> Fatal error:
> 14623 atoms are not part of any of the T-Coupling groups
> ==============================================
>  
> What I did is I first made .ndx file that include the protein atoms. 
> Then, I wrote this in the comand:
> grompp -f ----.mdp -c -----.gro -n ----.ndx -p ----.top -o ------.tpr
>  
> -----.mdp: I include the freeze option in this file.
> -----.ndx: This includes the group that I want to freeze.
> 1841: the total number of protein atoms.
> 116100: the total nuber of system atoms.
>  
> Could you please tell me what to do?
>  

You haven't included some large part of your system in the temperature coupling 
section.  All elements of the system have to be under the control of a 
thermostat.  Do not confusing the "freezing" method with something related to 
temperature; they are separate concepts.  If you need further help, post your 
full .mdp file.

-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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