[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 10 21:39:02 CET 2009

Chitrita Dutta Roy wrote:
> Hi Tsjerk,
> Did you mean to send you the md.mdp file that I used to run grompp for 
> md simulation? I am using Gromacs 4.0.2 versision. I am not very clear 
> about the parameters used in mdp files. So I am sending the mdp file here.

Some consultation with the manual will provide you with the information to learn 
about these parameters.  They should not be set blindly!

 > cpp                   =  /usr/bin/cpp

This is an example of one of the obsolete parameters no longer used in Gromacs 
4.0.x, hence grompp told you it would be ignored.

> Tcoupl                =  V-rescale
> tau_t                 =  0.1    0.1
> tc_grps               =  Protein    SOL
> ref_t                 =  300        300

Here is the problem, as grompp pointed out to you.  You are controlling the 
temperature of both the Protein and solvent water (SOL).  But your system 
contains NA+, doesn't it?  So it is not part of any temperature coupling group. 
  Try "Protein Non-Protein" for simple aqueous systems with ions.



Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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