**From:** Massimiliano Porrini (*M.Porrini_at_ed.ac.uk*)

**Date:** Thu May 26 2011 - 14:00:49 CDT

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Dear Nicholas and Jim,

Thank you for your useful replies.

Yesterday I tried with the basis vectors given in the link suggested

by Nicholas and

it worked.

Today I tried also the ones given by Jim and it worked as well.

But the two matrices differ by the sign of some elements (as you can see)

Does anybody know if there is a way to demonstrate that the two matrices are

equivalent?

Am I on the safe side if I choose one or the other?

Many thanks in advance,

MP

2011/5/25 Jim Phillips <jim_at_ks.uiuc.edu>:

*>
*

*> I think you have the matrix transposed. Try it like this:
*

*>
*

*> cellBasisVector1 $xx $yx $zx
*

*> cellBasisVector2 $xy $yy $zy
*

*> cellBasisVector3 $xz $yz $zz
*

*>
*

*> Try loading the original structure into VMD and using the draw line command
*

*> as in the code below to draw your original and swapped basis vectors. The
*

*> swapped (green) basis vectors should be orthogonal to the facets of the
*

*> original cell.
*

*>
*

*> -Jim
*

*>
*

*>
*

*>
*

*> set dist 58.9627607
*

*>
*

*> set xx [ expr $dist ]
*

*> set xy [ expr $dist * 1/3 ]
*

*> set xz [ expr $dist * -1/3 ]
*

*>
*

*> set yx [ expr 0 ]
*

*> set yy [ expr $dist * sqrt(2) * 2/3 ]
*

*> set yz [ expr $dist * sqrt(2) * 1/3 ]
*

*>
*

*> set zx [ expr 0 ]
*

*> set zy [ expr 0 ]
*

*> set zz [ expr $dist * sqrt(6) * 1/3 ]
*

*>
*

*> set o [list 29.295766830444336 29.650468826293945 29.59993553161621]
*

*>
*

*> set a [list $xx $xy $xz]
*

*> set b [list $yx $yy $yz]
*

*> set c [list $zx $zy $zz]
*

*>
*

*> draw color white
*

*> draw line $o [vecadd $o $a]
*

*> draw line $o [vecadd $o $b]
*

*> draw line $o [vecadd $o $c]
*

*> draw line $o [vecsub $o $a]
*

*> draw line $o [vecsub $o $b]
*

*> draw line $o [vecsub $o $c]
*

*>
*

*> puts [veclength $a]
*

*> puts [veclength $b]
*

*> puts [veclength $c]
*

*>
*

*> set a2 [list $xx $yx $zx]
*

*> set b2 [list $xy $yy $zy]
*

*> set c2 [list $xz $yz $zz]
*

*>
*

*> draw color green
*

*> draw line $o [vecadd $o $a2]
*

*> draw line $o [vecadd $o $b2]
*

*> draw line $o [vecadd $o $c2]
*

*> draw line $o [vecsub $o $a2]
*

*> draw line $o [vecsub $o $b2]
*

*> draw line $o [vecsub $o $c2]
*

*>
*

*> puts [veclength $a2]
*

*> puts [veclength $b2]
*

*> puts [veclength $c2]
*

*>
*

*>
*

*>
*

*> On Wed, 25 May 2011, Massimiliano Porrini wrote:
*

*>
*

*>> Dear all,
*

*>>
*

*>> I am trying to simulate a small protein immersed in a truncated
*

*>> octahedron box of water molecules.
*

*>>
*

*>> Basically I built the box via tleap program of Amber10 and then (using
*

*>> the vectors component
*

*>> taken from Gromacs manual) I passed the box parameters to NAMD config
*

*>> files in the
*

*>> following way (the "cellOrigin" values were obtained via VMD):
*

*>>
*

*>>
*

*>> 1) MINIMIZATION:
*

*>>
*

*>> ***
*

*>> # Periodic Boundary Conditions
*

*>> set dist 58.9627607
*

*>>
*

*>> set xx [ expr $dist ]
*

*>> set xy [ expr $dist * 1/3 ]
*

*>> set xz [ expr $dist * -1/3 ]
*

*>>
*

*>> set yx [ expr 0 ]
*

*>> set yy [ expr $dist * sqrt(2) * 2/3 ]
*

*>> set yz [ expr $dist * sqrt(2) * 1/3 ]
*

*>>
*

*>> set zx [ expr 0 ]
*

*>> set zy [ expr 0 ]
*

*>> set zz [ expr $dist * sqrt(6) * 1/3 ]
*

*>>
*

*>> cellBasisVector1 $xx $xy $xz
*

*>> cellBasisVector2 $yx $yy $yz
*

*>> cellBasisVector3 $zx $zy $zz
*

*>>
*

*>> cellOrigin 29.295766830444336 29.650468826293945
*

*>> 29.59993553161621
*

*>> ***
*

*>>
*

*>>
*

*>> 2) HEATING:
*

*>>
*

*>> ***
*

*>> # Continuing a job from the restart files
*

*>> binCoordinates $inputname.restart.coor
*

*>> extendedSystem $inputname.restart.xsc
*

*>>
*

*>> # Restraints
*

*>> constraints on
*

*>> consref $filename.pdb
*

*>> consKfile $filename.pdb
*

*>> consKcol O
*

*>>
*

*>> # Periodic Images
*

*>> wrapNearest on
*

*>> wrapWater on
*

*>> wrapAll on
*

*>> ***
*

*>>
*

*>>
*

*>> Hence at the end of these two processes I should get exactly the same
*

*>> box shape and
*

*>> dimensions as the one created via tleap (I am using an NVT esemble), but
*

*>> instead, as you can see from the linked figures, the shape is different,
*

*>> since
*

*>> the one obtained after NAMD minimization and heating appears to be
*

*>> "flatter":
*

*>>
*

*>> http://www.4shared.com/photo/9kN_g9Qi/amber.html
*

*>> http://www.4shared.com/photo/CKpojNEP/namd.html
*

*>>
*

*>> Do you kindly have any idea/hint about this behaviour?
*

*>>
*

*>> Should I be worried about a possible rotation of the protein and thus
*

*>> a likely interaction with a periodic image of its?
*

*>>
*

*>> Many thanks in advance.
*

*>>
*

*>> All the best,
*

*>> MP
*

*>>
*

*>> PS: as one can see from the displayed axes in the two enclosed figures,
*

*>> the orientation of the system is exactly the same, and the "suspected
*

*>> contraction" occurs along the z axis.
*

*>>
*

*>>
*

*>> --
*

*>> Dr Massimiliano Porrini
*

*>> P. E. Barran Research Group
*

*>> Institute for Condensed Matter and Complex Systems
*

*>> School of Physics & Astronomy
*

*>> The University of Edinburgh
*

*>> James Clerk Maxwell Building
*

*>> The King's Buildings
*

*>> Mayfield Road
*

*>> Edinburgh EH9 3JZ
*

*>>
*

*>> Tel +44-(0)131-650-5229
*

*>>
*

*>> E-mails : M.Porrini_at_ed.ac.uk
*

*>> mozz76_at_gmail.com
*

*>> maxp_at_iesl.forth.gr
*

*>
*

-- Dr Massimiliano Porrini P. E. Barran Research Group Institute for Condensed Matter and Complex Systems School of Physics & Astronomy The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ Tel +44-(0)131-650-5229 E-mails : M.Porrini_at_ed.ac.uk mozz76_at_gmail.com maxp_at_iesl.forth.gr

**Next message:**David Huggins: "TIP5P water simulation"**Previous message:**Jérôme Hénin: "Re: vmd-l: measure fit - wrong alignment"**In reply to:**Jim Phillips: "Re: Truncated octahedron box issues (?)"**Next in thread:**Jim Phillips: "Re: Truncated octahedron box issues (?)"**Reply:**Jim Phillips: "Re: Truncated octahedron box issues (?)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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