[gmx-users] reg PME usage

[Mark Abraham]

On 13/06/2011 6:18 PM, vidhya sankar wrote:
> Dear mark,
>                  I am Typing  the Literature Word, as such
> Although the PME is prefered way to treat Long rang electrostatic 
> interaction
>  it was not used Here Since the overall Charge of Solvated system Had 
> non zero value (-12)
>

Google around - this issue has been discussed in many places already.

> Also counter ion usually NA+ and CL- added to Neutralize the system 
> Would interfere the system.
>

Why? Was that a reasonable model of their system? Does that apply to 
your problem?

> The Non bonded interaction were treated using a set of Cutoffs 
> .Distance Cutoff in generating the list of pairs was set to 12.0 
> Amstrong .
> At 11 Amstrong the switching function Eliminated  all the contribution 
> to the overall energy  from pairwise interactions  At.10 Amstrong the 
> smoothing function began to reduce pair's contribution
>
> How could i implement the above protocol for my system in  .mdp file
>

By reading the manual sections that describe the interaction algorithms 
and parameters that work in them, and doing tutorial material to see 
some things in action - even if they're not things you think you want now.

Mark
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