[gmx-users] position restraining of ions

soumadwip ghosh soumadwipghosh at gmail.com
Wed Jul 15 18:59:06 CEST 2015

   this problem usually arises when there are more than one species of
a perticular kind is present in your conf.gro file. In your case you
have 85 potassium and 122 chloride ions in the input .gro file you
used while generating individual ion posre.itp files. However, in the
ions.itp file in your FF directory contains one description for K+ and
CL- each. If you observe carefully,grompp complains about atomindex
starting from 2 that's because genrestr made posre.itp for all the
potassium ions in the system ( same with chloride) while in ions.itp
there is only one description of both K+ and and CL- .

I think the following will help

1. make an index file containing one K+ and one CL-
2. Issue genrestr with -n flag
3. when prompted use these two indices with one residue each separately
4. Make separate posre.itp for both the species
5. They should not contain more than a line
6. Include these two .itp files with proper IFDEF statements in the system.top .

I dont think you will see the error after this.


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