[gmx-users] DNA orientation restrain

[lina]

On Monday 01,October,2012 01:44 PM, 仝督读 wrote:
> 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,

notice the posre.itp?

; atom  type      fx      fy      fz
     1     1  1000  1000  1000
     5     1  1000  1000  1000


change the fz value to be high enough, like below:

1     1  1000  1000  50000

this 50000 I just made up here as example, you may try to pick a
reasonable one.
> 
> Dudu Tong
> <31%2032%201%201%203%203>