protein shifts out of water box

From: Kwee Hong (
Date: Tue Aug 31 2010 - 05:20:53 CDT

Hi all,

I've subjected my protein to 1ps energy minimization, before equilibrating
the temperature and pressure. Then the protein is subjected to a 1ns MD run.
The periodic boundary and PME condition in the configuration file was
determined with the following script:

# Periodic Boundary Conditions
set sel [atomselect top all]
set cen [measure center $sel]
set mm [measure minmax $sel]
set vmin [lindex $mm 0]
set vmax [lindex $mm 1]
set vdif [vecsub $vmax $vmin]
set xx [lindex $vdif 0]
set yy [lindex $vdif 1]
set zz [lindex $vdif 2]
set cenx [lindex $cen 0]
set ceny [lindex $cen 1]
set cenz [lindex $cen 2]
set padding 0
# PME (for full-system periodic electrostatics)
package require pmepot
set gridsizex [::PMEPot::good_fft_dim $xx]
set gridsizey [::PMEPot::good_fft_dim $yy]
set gridsizez [::PMEPot::good_fft_dim $zz]
puts "TO_NAMD:cellBasisVector1 [expr $xx+$padding] 0. 0."
puts "TO_NAMD:cellBasisVector2 0. [expr $yy+$padding] 0."
puts "TO_NAMD:cellBasisVector3 0. 0 [expr $zz+$padding]"
puts "TO_NAMD:cellOrigin $cenx $ceny $cenz"
puts "TO_NAMD:wrapAll on"
puts "TO_NAMD:PME yes"
puts "TO_NAMD:PMEGridSizeX $gridsizex"
puts "TO_NAMD:PMEGridSizeY $gridsizey"
puts "TO_NAMD:PMEGridSizeZ $gridsizez"

cellBasisVector1,2,3 and cellOrigin was determined at the energy
minimization and equilibrating temperature stage only as extendedSystem was
used in the later steps (equilibrating the pressure and md run). While
PMEGridSizeXYZ were determined at every steps with the above scripting. I
wonder is this protocol correct? Would it be something that I missed here
which causes me to have my protein shifted out from the waterbox at the end
of the simulation?



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