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
--
========================================
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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