[gmx-users] tip5p.gro

[Mark Abraham]

On 15/04/2011 12:04 AM, sarah k wrote:
> Dear Justin,
> I found out that as you had said, my naming wasn't consistent. I 
> checked and manipulated all file in share/top. i didn't have any 
> problem with files flexwaterguson.itp, atommass.dat, spc.itp, 
> spce.itp, spc216.gro and tip3.itp but when it comes to files tip4p.gro 
> and tip5p.gro I hang. These files are equilibrated in NPT simulation 
> @300 K with PME. The SOL molecules have 4! atoms and there are 6 
> coordinations for each atom. How can I guess the Nitrogen values to 
> replace them? Again, thanks in advanced!

Forget about trying to replace molecules in an existing solvent box. The 
density will be wrong even if you succeed. A few days ago I pointed you 
obliquely to a genconf solution. Here's an actual link 
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060007.html

Mark