[gmx-users] Umbrella Sampling _ pulled ion

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jul 24 17:30:42 CEST 2013


I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane.

In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file:
pull_group1     = Ces_ion

So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) :

[ system]

[ Ces_ion ]

But after running the grompp, I get this fatal error:
File input/output error:

Would you please let me know how I would be able to define a new group for a specific ion ?
Did I make a mistake in defining a new group? 
Would you please give me any suggestions?

Thanks in advance,

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