**From:** Jim Phillips (*jim_at_ks.uiuc.edu*)

**Date:** Thu May 26 2011 - 22:59:06 CDT

**Next message:**David McGiven: "NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE""**Previous message:**David Huggins: "TIP5P water simulation"**In reply to:**Massimiliano Porrini: "Re: Truncated octahedron box issues (?)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Given the symmetry of the lattice you can probably change any of the signs

without affecting the Weigner-Seitz primitive cell (i.e., wrapNearest).

-Jim

On Thu, 26 May 2011, Massimiliano Porrini wrote:

*> 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 McGiven: "NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE""**Previous message:**David Huggins: "TIP5P water simulation"**In reply to:**Massimiliano Porrini: "Re: Truncated octahedron box issues (?)"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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