[gmx-users] Different fudge scaling against the default ones

Chandan Choudhury iitdckc at gmail.com
Thu Sep 25 08:34:55 CEST 2014

Dear gmx users,

I see the following lines in the forcefield.itp file of amberGS.ff (gmx
466) (share/gromacs/top/amberGS.ff/) :

#define _FF_AMBER
#define _FF_AMBER94

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             1.0     0.8333
1               2               yes             0.5     0.8333

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gbsa.itp"

For the defaults section, it seems that it is possible to use different
fudge scaling (1.0, 0.833) against the default ones (0.5, 0.8333).
The default one gets selected automatically. I think one needs add a line in
.mdp file, but I do not know what needs to be done for selection the
different one.

Can anyone shed light on it?



Chandan Kumar Choudhury
National Chemical Laboratory, Pune

*"All work and no play makes Jack a dull boy...”*

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