Hi, Depending on what you aim to do one option might be to make the DNA a pair of periodic molecules. That would keep them aligned with whatever box vector you chose. But again, that depends on what you aim to study.
Erik 1 okt 2012 kl. 07.44 skrev 仝督读: > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
