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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