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

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Fri Oct 22 15:30:00 CEST 2010

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?

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?
Could I use, for example, _FF_GROMOS53A6, or that is only posible if I  
use before: _FF_GROMOS96 ?

Thank you in advance.

Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221

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