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
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