VMD-L Mailing List
From: Jim Parker (jimparker96313_at_gmail.com)
Date: Sat Dec 13 2014 - 15:02:17 CST
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- In reply to: Jim Parker: "Re: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc"
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All,
Just closing the book on this. Bottom line was user error. I was using
a VMD tcl script to get the size of the box
set meas [measure minmax $sel ]
set x [expr { [lindex [lindex $meas 1] 0] - [lindex [lindex $meas 0] 0]
} ]
set y [expr { [lindex [lindex $meas 1] 1] - [lindex [lindex $meas 0] 1]
} ]
set z [expr { [lindex [lindex $meas 1] 2] - [lindex [lindex $meas 0] 2]
} ]
but in my simulations of the NPT ensemble usng NAMD and PBC, I had enabled
"wrapAll". The "wrapped" atoms generate a less dense overlap region that
is included in the measure minmax box size
If you use
set cell [molinfo $molid get {a b c} frame $frame]
you will get the actual dimensions of the periodic cell, and an appropriate
volume and density.
Cheers,
--Jim
- Next message: Axel Kohlmeyer: "Re: FFTK most probably doesn't work with molecules containing new atom types"
- Previous message: Josh Vermaas: "Re: FFTK most probably doesn't work with molecules containing new atom types"
- In reply to: Jim Parker: "Re: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc"
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