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.u...@gmail.com> > An: gmx-users@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> > -- > 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 -- 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
