[gmx-users] problem regarding grompp

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 18 13:07:36 CET 2008

kinshuk at chem.iitb.ac.in wrote:
> Hi all,
>  I have been trying to simulate peptide (octa alanine). In genbox i have
> inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
> maxsol option in gromacs 3.3.3)then again with genbox i added 40
> molecules of thiocynate ion & 80 water molecules as above mentioned way.
> When i tried to do grompp for energy minimization i was encountered with
> many warning listed below though i have included the *.itp files of both
> ions in the topology *.top file of peptide.I need some insight about this
> so that i can resolve this problem.
> I have attached the em.mdp file along with this mail.

This is not the problem, but your T-coupling groups aren't useful. See 

> If i will be getting help i'll be thankful for you.

The order of molecules in your .top files [ molecules ] section probably 
doesn't match the order of molecules in your structure file. See chapter 
5 of the GROMACS manual if you don't understand this.


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