Hi,
Putting ions as individual molecule is quite a standard practice.
Looking at ions.itp in the top directory. I added ions there with new
forcefield preprocessor directives. Most gromacs users except you will
get a low mark, I reckon.
I tried your way in the previous and just now. It works. You may use -pp
for your grompp and send me directly the output file if you are keen to
find more.
Yang Ye
D. Ensign wrote:
numbered consecutively
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Regarding addition of ions, apparently resulting in grompp error: Atoms in the
.top are
not numbered consecutively from 1
Try this:
1. Paste this at the place of my_ions.itp to replace it.
[ moleculetype ]
NA+ 1
[ atoms ]
1 amber99_31 1 NA+ NA+ 1 1 22.99000
[ moleculetype ]
CL- 1
[ atoms ]
1 amber99_30 1 CL- CL- 1 -1 35.45000
2. Replace "Ions 1" with
Na+ 6
Cl- 2
Why, yes, that seems to work. How interesting.
However, your solution suffers from the problem that it is much simpler and
easier to
implement than mine. You get an A-. ;)
Seriously, though, this is interesting. When I run genion on a system, then
afterwards
rebuild it with pdb2gmx, it places the ions before the solvent, and places their
topologies in topol_B.itp. Further, in topol_B.itp they are listed as one
"molecule" with
no bonds, and indicated in topol.top as one "molecule."
Your solution, on the other hand, makes each ion its own molecule. I like it,
but I'm
wondering what's going on.
Dan Ensign
Stanford University
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