[gmx-users] T-coupling problem?

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 20 23:43:10 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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