[gmx-users] The solvent group Water is not continuous

[Mark Abraham]

On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
> Dear Justin,
>
> I have Fatal Errror:The solvent group Water is not continuous. I look 
> at gmx-users mailing list search. I also have the same problem.
> You 
> said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
> It is exactly what I said; you've proven it. You have solvent, ligand, then
> solvent. To use genion (as the program prints out at the prompt) you must have
> a *continuous* group of solvent in order to embed ions. If you re-arrange the
>
> coordinate file and [molecules] section of the topology, you can achieve this.
>
> How can I do the re-arrange you said? Can you explain a little bit?

You need a system topology whose molecules are ordered such that all the 
water is contiguous. That means the order of the names of molecule types 
in your [ molecules ] section of your .top can have only one mention of 
water. Since the order of molecules in the coordinate file must match 
this order, you will need to physically reorder your [ molecules ] 
section, and the chunks of molecules in your coordinate file. 
Fortunately, you don't have to renumber those atoms in the coordinate file.

Mark