[gmx-users] T-coupling problem?

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 21 01:06:12 CET 2012

On 21/02/2012 8:39 AM, 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:

A more sound protocol for preparation for MD probably involves the use 
of position restraints, rather than frozen atoms. See various tutorials 
for examples.

> ==============================================
> 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

Copying and pasting actual command lines is preferred by those who might 
give feedback. They want to see what actually happened, not what you 
think happened.

> -----.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.

116100 < 14623. Some part of your report is badly wrong.


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