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On 13/06/2011 6:18 PM, vidhya sankar wrote:
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<td style="font: inherit;" valign="top">Dear mark,<br>
I am Typing the Literature Word, as such<br>
<span style="font-weight: bold;">Although the PME is
prefered way to treat Long rang electrostatic
interaction<br>
it was not used Here Since the overall Charge of
Solvated system Had non zero value (-12) </span></td>
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<br>
Google around - this issue has been discussed in many places
already.<br>
<br>
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<td style="font: inherit;" valign="top"><span
style="font-weight: bold;">Also counter ion usually NA+
and CL- added to Neutralize the system Would interfere
the system.</span></td>
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<br>
Why? Was that a reasonable model of their system? Does that apply to
your problem?<br>
<br>
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<td style="font: inherit;" valign="top"><span
style="font-weight: bold;">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 .<br>
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</span><br>
<br>
How could i implement the above protocol for my system in
.mdp file <br>
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<br>
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.<br>
<br>
Mark<br>
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