Dear Skrynnikov,
To substract translational motion, which I assume means translation of
the entire molecules, one can keep the centre of mass at the origin (of
the PDB-frame)
Another option (which is simpler, but has the restriction that only one
molecule can be used) is to fix the coordinate of one atom of your
molecule in space. The parameter-file prevents the molecule from falling
apart.
Below this line the syntax that could be used in a script.
I hope this is any help to you.
Kind regards,
Ramon van der Werf
Centre of mass option:
-----------------------
{*calculate centre of mass vector *}
COORmanipulation RGYRation SELEction=(all) end
!vector stored under $XCM,$YCM,$ZCM
{*Translate to origin*}
COORmanipulation TRANslate VECTor (-$XCM,-$YCM,-$ZCM)
Fixing one atom in space option:
-----------------------------------
CONStraints FIX=(resid. # and name ##) end
Note: this fix statement is active untill another fix statement is
called. To undo fix later on in a script:
CONStraints FIX=(not all) end
On Sun, 2008-02-17 at 12:00 -0500, xplor-nih-request at nmr.cit.nih.gov
wrote:
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> Today's Topics:
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> 1. Re: subtracting out translation (Nikolai Skrynnikov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 16 Feb 2008 12:56:36 -0500
> From: Nikolai Skrynnikov <nikolai at purdue.edu>
> Subject: Re: [Xplor-nih] subtracting out translation
> To: xplor-nih at nmr.cit.nih.gov
> Cc: Yi Xue <yixue at purdue.edu>, Nathan Benjamin
> <nathansbenjamin at gmail.com>
> Message-ID: <47B723D4.3000600 at purdue.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> We would like to subtract out protein's translational motion, but retain
> rotational motion (assuming that with tcoupling=true the protein is not
> going to spin out of control). We tried a few things, below is the version
> which seemed like our best bet:
>
> evaluate($count=1)
>
> while (2>1) loop write
> evaluate ($TRAJECTORY = "traj_"+encode($count)+".dcd")
> dynamics torsion
> ntrfrq = 0
> timestep = 0.002
> nstep = 5000
> tcoupling = true
> tbath = 300
> nprint = 500
> iprfrq = 0
> asci = false
> nsavc = 500
> traj = $TRAJECTORY
> end
> evaluate ($count=$count+1)
> coor copy sele=(all) end
> coor orient sele=(all) end
> display $x $y $z
>
> coor swap sele=(all) end
> vector do (x=x+$x) (all)
> vector do (y=y+$y) (all)
> vector do (z=z+$z) (all)
> {* alternaitvely coor translate sele=(all) vector=($x,$y,$z) end *}
> end loop write
>
>
> The printout from this script seems fine, but it actually fails to
> reset the coordinates to (0,0,0) in between the frames as we hoped...
>
> Many thanks ahead of time!
>
> Cheers,
>
> Nikolai
>
