[gmx-users] Topology and force fields

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 5 20:05:05 CEST 2010

Gareth Tribello wrote:
> Hello
> 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 

That is exactly what was in the original topology, no problem there.  There are 
no [atomtypes] in tip3p.itp; these are defined by ff*nb.itp.

> 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.

More likely grompp will raise a fatal error that the atomtypes are not found, 
before anything else happens :)

You could, in theory, run a simulation of just water by specifying a all the 
directives listed at the parameter level (Table 5.3 and section 5.7.1 in the 
manual) in the .top file, then #include "tip3p.itp" - that's all that's really 
necessary.  Using the #include mechanism with an existing force field solves 
this problem for you.  The combination rules of the Gromos, OPLS, and CHARMM 
force fields are all different (manual section 5.3.3, equations 5.3 and 5.4), 
but I don't know offhand what effect that might have on your results.

TIP3P itself is not really a force field, it is a set of parameters that model a 
single molecule.  The interaction function (the other part of a force field) is 
defined by the functional forms defined by ff*.itp in the parameter-level 
directives.  Otherwise, the atom types and nonbonded parameters for a water 
model should be uniform, that is, independent of the force field chosen (with 
the only modifications being conversion between sigma/epsilon and C6/C12, per 
force field requirements).  Your treatment of other .mdp parameters will affect 
your results, as well, but many of these should be prescribed in the derivation 
of the parameters or in subsequent modifications and extensions.


> ciao
> Gareth
> On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi <lumngwegia at gmail.com 
> <mailto: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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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