[gmx-users] Subject: basic questions about _FF_FORCEFIELD statement.....

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 22 16:03:37 CEST 2010

Alberto Sergio Garay wrote:
> Dear gmx-users
> I have some very basic questions about the following statements:
> #define _FF_GROMACS
> #define _FF_GROMACS1
> [ defaults ]
> ; nbfunc        comb-rule  gen-pairs fudgeLJ fudgeQQ
>   1             1          no        1.0     1.0
> #include "ffnonbonded.itp"
> #include "ffbonded.itp"
> 1) What does this statement mean? (#define  _FF_GROMACS)
> The gromacs' manual says:
> ?That it can be used in topologies to parse data which is speci?c for 
> force ?elds?
> Does this mean that gromacs will use the Potential Energy Analytical 
> Function (PEAF) for this forcefield (gromacs forcefield)?
> If my first guess was correct (or at least in part)...
> How does gromacs manage gromos analytical function when we define the 
> corresponding option in the parameter files (e.g.: using the option 2 
> for the angle potential parameters). Does it transform the given 
> parameters from gromos to gromacs in order to reproduce the same 
> behavior for that angle?

I'm not sure what transformations you're referring to.  Functional forms, units, 
and parameters are all discussed in the manual.  In any case, you can look in 
the source code for a definitive answer :)

> 2) What does this statement mean? (#define  _FF_GROMACS1)
> The gromacs' manual says:
> ? That is to parse data speci?c to this force ?eld?
> Could you give me an example of what kind of data it is parsing when we 
> use this statement?

See, for instance, spc.itp:

#ifdef _FF_GROMACS
#include "gmx.ff/spc.itp"
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/spc.itp"
#ifdef _FF_OPLS
#include "oplsaa.ff/spc.itp"

The #define statements allow the topology to be parsed appropriately, to 
#include only the relevant parameters.  This mechanism used to be used in 
ions.itp, as well, but became obsolete with the force field reorganization in 
version 4.5.


> Could I use, for example, _FF_GROMOS53A6, or that is only posible if I 
> use before: _FF_GROMOS96 ?
> Thank you in advance.
> Sergio


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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