[gmx-users] how to constrain a dihedral
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 8 09:00:07 CET 2004
On Wed, 2004-12-08 at 11:17 +0800, mengyi wrote:
> Hi all
> there are two question:
> (1) i want to constrain some dihedrals during MD,
> such as
> 1 4
> \ /
> i want keep [1 2 3 4] planar, how can i do it?
If you want to have them analytically planar you have to use dummies. If
a restraint is enough useimproper dihedrals (chpater 4)
> (2) when i use constraints=h-angles, algorithm=shake, it always crash.
> but if i use constraints=h-bonds there is no problem. why? is there something
> need to do before using angle-constraint?
I assume you mean mdrun crashes? It shouldn't, but check time step.
> thanking you all in advance
> --ȶɿĵ ʼ ƶǩ 洢...δ
> --¼VIP עû
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users