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

[Justin A. Lemkul]

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 
> all GROMACS
> 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"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/spc.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/spc.itp"
#endif

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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