[gmx-users] DNA orientation restrain

[Erik Marklund]

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 at 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-request at 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
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html