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<p class=MsoNormal>Dear all,<o:p></o:p></p>
<p class=MsoNormal>I am a bit confused about how the pair potentials (PPs)are
calculated.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>If I state explicitly sigma and epsilon values for the pair
potentials, can I then still have a coulomb scaling of my 1-4 interactions?<o:p></o:p></p>
<p class=MsoNormal>Say I set “gen-pairs” to “yes”,
although I have all possible pair potential interactions specified under “[
pairtypes ]”, would I then still be able to scale my 1-4 coulomb
interactions by setting a “FudgeQQ” different from 1? Also, would I
be able to scale the already given van der Waals interactions with “FudgeLJ”?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Finally, are generated pair potentials based on the parameters
specified under “[ atomtypes ]” or “[ nonbond_params ]”
(if the latter exist) in the ffamber03nb.itp file?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Best regards,<o:p></o:p></p>
<p class=MsoNormal>Soren Enemark<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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