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> -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists