[gmx-users] Topology and force fields

Gareth Tribello gareth.tribello at gmail.com
Mon Apr 5 19:35:36 CEST 2010


I think what you have been told is wrong.  You need to include both
"ffcharmm27.itp" and "tip3p.itp" as the atomtypes in your tip3p.itp will
otherwise not be defined.  There is an easy way to check though - take out
the include ffcharmm27.itp and try to run grompp on your new topology.  My
bet would be that it won't work and, if you are using rigid molecules, it
will tell you that it finds a settles section in the wrong place.


On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi <lumngwegia at gmail.com> wrote:

> Hello all,
>         Below are the contents of a water1.top file that I used to simulate
> 2000 molecules of TIP3P water (NPT).  I made this topology file according to
> the pattern on page 114 of the manual (topology for Urea in water). My
> diffusion coefficient, viscosity and radial distribution functions matched
> those for tip3p water in literature.
>         Recently I was told that I did not need to use another force field
> in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield
> on its own. Could this be true? I just wanted to verify the authenticity of
> my simulation. If the structure of the topology below is not correct, please
> let me know.
> ; The force field files to be included
> #include "ffcharmm27.itp"
> ; Include TIP3P water topology
> #include "tip3p.itp"
> [ system ]
> Pure Water
> [ molecules ]
> ;molecule name number
> SOL              1936
> SOL                64
> I appreciate your answers.
> Lum
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