Wednesday, November 23, 2011

NAMD inputs from VMD

set all [atomselect top all]
measure minmax $all
set cellxmin [lindex [lindex [measure minmax $all] 0] 0]
set cellxmax [lindex [lindex [measure minmax $all] 1] 0]
set cellymin [lindex [lindex [measure minmax $all] 0] 1]
set cellymax [lindex [lindex [measure minmax $all] 1] 1]
set cellzmin [lindex [lindex [measure minmax $all] 0] 2]
set cellzmax [lindex [lindex [measure minmax $all] 1] 2]

puts "cellOrigin              [format "%7.3f %7.3f %7.3f" [lindex [measure center $all] 0] [lindex [measure center $all] 1] [lindex [measure center $all] 2]]"
puts "cellBasisVector1        [format "%7.3f %7.3f %7.3f"      [vecsub $cellxmax $cellxmin] 0 0]"
puts "cellBasisVector2        [format "%7.3f %7.3f %7.3f"  0   [vecsub $cellymax $cellymin] 0]"
puts "cellBasisVector3        [format "%7.3f %7.3f %7.3f"  0 0 [vecsub $cellzmax $cellzmin] ]"



Pretty primitive, but it works.

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