[gmx-users] DNA orientation restrain

lloyd riggs lloyd.riggs at gmx.ch
Mon Oct 1 21:48:17 CEST 2012

Dear Dudu Tong

Theres a paper on using limited x y z restraints but I have forgotten it.  In any case theres a way to generate 1 2 or 3D positional restraints with just the grompp , and you can cut and past.  The output posre in the help command will give you a file, and theres a selection for what force you want applied , but If you want only 1 or 2 dimensions you just need a spread sheet editor, and can change 1 or 2 manually after they are generated.

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Mon, 1 Oct 2012 13:44:20 +0800
> Von: "仝督读" <tongdudu.ustc at gmail.com>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] DNA orientation restrain

> Hi everyone,
> I am doing a DNA simulation in a long simulation box (the lengthen of z is
> much larger than x and y). So I want to constrain the DNA molecule lying
> along the z axis. But I don't know how to realize this in GROMACS.
> Actually I notice there is orientation restraints in 4.3.5 of GMX Manual.
> But the orientation value is set to be observables of NMR experiments,
> such
> as this example:
> ; ai aj type exp. label alpha const. obs. weight
> 31 32 1  1  3  3  6.083  -6.73  1.0
> But how can I set the observable in my case as it's not an NMR experiment?
> Any suggestion will be appreciate.
> Thanks very much
> Dudu Tong
> <31%2032%201%201%203%203>
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