[gmx-users] Problems with DNA simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 20 15:32:58 CEST 2009

Gunnar Widtfeldt Reginsson wrote:
> Hi. I am new to Gromacs and I am  following the tutorial 
> on http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top
> I have managed to get the DNA into a water box. When I run genbox  I use 
> the ffamber_tip4p.gro water model.
> When I then run:
> grompp -f neutralize.mdp -c solved.pdb -p topol I get this fatal error:
> where neutralize.mdp is from the website above.
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: readir.c, line: 1463
> Fatal error:
> Invalid T coupling input: 0 groups, 2 ref_t values and 2 tau_t values
> -------------------------------------------------------
> I have been searching for an explanation to this error but haven't found 
> anything. Can somone please help. 

Not without seeing the relevant section of your .mdp file, but it looks like you 
  haven't actually specified any groups to be subject to temperature coupling.


> Thanks.
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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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