VMD-L Mailing List

From: Matteo Guglielmi (matteo.guglielmi_at_epfl.ch)
Date: Thu Oct 18 2007 - 14:07:16 CDT

Dear All,

I need also to rotate the water molecules for my
QM/MM setup (or at least some of them which
were very important)... anyway, the solution I
have found was to place (9x3-1) replicas all
around my initial box.

Than I did rotate the all thing like if it was a
single rigid body... and than, finally, I did select
and kept only the molecules which were 'still'
inside the original 'volume'.

Since the periodicity was broken, I had also to
re- equilibrate the box keeping frozen the protein
and some buried water molecules.

Thanks for your answers anyway guys!

Matteo.

Jan Saam wrote:
> Dear Matteo,
>
> you cannot rotate molecules in PBC cells without breaking the linkage
> between the cells.
> Think about a brick wall were each brick represents a molecule (or
> better your atoms in the PBC box): Rotating the box corresponds to
> rotating each single brick around its center - what will happen to the
> wall?!
>
> You could in principle rotate the entire wall, which means that you
> rotate the molecule *and* the pbc vectors, but there are restrictions
> on the pbc vectors (by definition): A has to be parallel to the X
> axis, B has to be in the XY-plane.
>
> The only rotations that make sense for a PBC cell that come to my mind
> are the following:
> After you align all frames of a trajectory your PBC cell linkages will
> be messed up. Suppose you want to know which atoms are close to one
> atom X which is close to the box fringe, i.e. you need the positions
> of the atoms in the neighboring cells. In this case you can create a
> copy of your box and move it according to the *rotated* PBC vectors.
> Then you'll get the atoms in the neighboring box in the correct
> relative position to your original box. Rotated PBC vectors means that
> you rotate them with the same matrix that was used to align the
> corresponding frame.
>
> I asssume that you simply wanted a different orientation of your
> molecule after you solvated it. You will achieve this if you first
> rotate your molecule to the prefered orientation and solvate it after
> that.
>
> I hope this helps,
>
> Jan
>
>
>
> John Stone schrieb:
>> Hi,
>> I'd suggest asking the PBCTools plugin authors about the
>> correct way to do this given that the rotations you're performing
>> seem to be conflicting (at least from your description) with the
>> operations done by the PBC plugin in the calls your making.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Tue, Oct 09, 2007 at 02:02:34PM +0200, Matteo Guglielmi wrote:
>>
>>> Dear All,
>>>
>>> recently I did try to rotate a protein fully
>>> solvated by water molecules using the 'pcb'
>>> plugin and the following simple script:
>>>
>>> # pdb file header:
>>> # CRYST1 111.108 98.438 115.981 90.00 90.00 90.00
>>> set sys [mol new RUN01.pdb]
>>> set all [atomselect $sys all]
>>> set com [measure center $all]
>>> # 55.5484428406 49.2036247253 58.0394554138 ('set com...' outcome)
>>> $all moveby [list -55.5484428406 -49.2036247253 -58.0394554138]
>>> pbc set {111.108 98.438 115.981 90.00 90.00 90.00} -now
>>> pbc box -center origin
>>> set delta_deg 0.01
>>> # rotate x by -15 deg
>>> for {set x 0} {$x>-15} {set x [expr {$x - $delta_deg}]} {
>>> $all move [transaxis x -$delta_deg]
>>> pbc wrap -center origin
>>> }
>>> # rotate y by 40 deg
>>> for {set x 0} {$x<40} {set x [expr {$x + $delta_deg}]} {
>>> $all move [transaxis y $delta_deg]
>>> pbc wrap -center origin
>>> }
>>> # rotate z by -55 deg
>>> for {set x 0} {$x>-55} {set x [expr {$x - $delta_deg}]} {
>>> $all move [transaxis z -$delta_deg]
>>> pbc wrap -center origin
>>> }
>>> $all writepdb rotated.pdb
>>>
>>>
>>> .... well, the pbc box was correctly placed
>>> on top of the simulation box (volume) but
>>> the resulting 'rotated.pdb' was not good at
>>> all (water molecules close to the box edges
>>> got wrongly placed in the 'rotated.pdb' file)
>>>
>>> To see the weird effect just try the script with
>>> a simple water box.
>>>
>>> Do you know any better way to rotate a box
>>> with the pbc plugin?
>>>
>>> Best,
>>> MG.
>>>
>>
>>
>
> --
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> Germany
>
> +49 30 450-528-446
> saam_at_charite.de
> 

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