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

[Yang Ye]

Hi,

Normally force field will have exclusion of 1-3 interaction (I doubt the=20
intention of inclusion of 1-2 interaction will lead to destroy of=20
structure). I suggest you first try with excl (in molecule definition)=20
set to 3 and add entries under pair and see whether they are effective.=20
If this works, you will proceed add second set of parameters for pair=20
interaction.

If above does work, you will need to set excl to a lower number, turn=20
off generate pairs (in ffxxxx.itp) and list explicitly every pair that=20
you would like to include, both the normal 1-4 interactions and adjusted=20
1-2 and 1-3 interactions.

Ref to Manaul Table 5.3 and 5.4.

Regards,
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=20
> interactions between pairs of atoms in the [ pairs ] section and do=20
> free energy calculations by perturbing these interactions. If it is=20
> possible, how can I do that.Thank you.
> Kind Regards
> Yang Liu
>
>
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