[gmx-users] Can I add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions.

Yang Ye leafyoung at yahoo.com
Tue May 1 16:58:25 CEST 2007


Normally force field will have exclusion of 1-3 interaction (I doubt the 
intention of inclusion of 1-2 interaction will lead to destroy of 
structure). I suggest you first try with excl (in molecule definition) 
set to 3 and add entries under pair and see whether they are effective. 
If this works, you will proceed add second set of parameters for pair 

If above does work, you will need to set excl to a lower number, turn 
off generate pairs (in ffxxxx.itp) and list explicitly every pair that 
you would like to include, both the normal 1-4 interactions and adjusted 
1-2 and 1-3 interactions.

Ref to Manaul Table 5.3 and 5.4.

Yang Ye

On 5/1/2007 10:53 AM, intelandamd wrote:
> Dear
> I want to add extra LJ and electrostatic interactions for 1-2 or 1-3 
> interactions between pairs of atoms in the [ pairs ] section and do 
> free energy calculations by perturbing these interactions. If it is 
> possible, how can I do that.Thank you.
> Kind Regards
> Yang Liu
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