[gmx-users] DNA orientation restrain

仝督读 tongdudu.ustc at gmail.com
Mon Oct 1 07:44:20 CEST 2012

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

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