[gmx-users] DNA orientation restrain
lina.lastname at gmail.com
Tue Oct 2 06:00:03 CEST 2012
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
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
> Dudu Tong
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