From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 27 2003 - 13:22:52 CST
Hi,
The pairInteraction feature only covers direct electrostatic and vdw
interactions; i.e., not long-range electrostatics, bonding terms, etc.
However, it should be trivial to calculate interaction with an external
electric field using VMD. Something like:
set eField [list 10. 0. 0.]
set sel [atomselect top "protein"]
set eForce [list 0. 0. 0.]
set eEnergy 0.
foreach xyzq [$sel get {x y z charge}] {
foreach {x y z q} $xyzq break
set xyz [list $x $y $z]
set eForce [vecadd $eForce [vecscale $q $eField]]
set eEnergy [expr $eEnergy - $q * [vecdot $eField $xyz]]
}
puts "Energy: $eEnergy"
puts "Force: $eForce"
-Jim
On Sun, 19 Oct 2003, Ioana Cozmuta wrote:
> Hi,
>
> Is there an option to use the pairInteraction module to calculate the
> interaction energy and forces between a group of atoms and the external
> applied electric field (for the case when the MD was run with the external
> applied electric field turned on)?
>
> THank you,
> Ioana
>
>
>
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