[gmx-users] error during nvt equilibration

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 12:50:42 CET 2012

On 11/29/12 12:40 AM, Shine A wrote:
> Sir,
>     I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
> Now doing nvt equilibration and created index.ndx by using make_ndx. During
> this step I selected "16/14" and "1/13".The next step (grompp -f nvt.mdp -c
> em.gro -p topol.top -n index.ndx -o nvt.tpr) getting error like this
>   Fatal error:
> Group SOL_CL not found in indexfile.
> Maybe you have non-default goups in your .mdp file, while not using the
> '-n' option of grompp.
> In that case use the '-n' option.
>   why this error? Can you give a solution to overcome it?

You're using a group called "SOL_CL" in the .mdp file, but one is not found in 
the .ndx file.  If indeed you used "16/14" to make the necessary index group, 
that is wrong.  The syntax is a pipe (|) to merge groups, not a slash (/).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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