[gmx-users] rigid body again

[David van der Spoel]

On Thu, 2005-06-09 at 10:35 -0400, Lianqing Zheng wrote:
> Thanks, David! What is long range constraint? For an i-j-k-l dihedral,
> try to constrain i---l distance?
no, you  just define them yourself, from one end of the molecule to the
other.
> 
> Lianqing
> 
> 
> On Thu, 9 Jun 2005, David van der Spoel wrote:
> 
> >On Thu, 2005-06-09 at 10:19 -0400, Lianqing Zheng wrote:
> >> Dear gmxers,
> >> 
> >> I have checked the archive and it seems gmx is not directly supporting
> >> rigid molecule simulation. I'm wondering if the following will work.
> >> 
> >> Say, for a molecule of N atoms, we choose 3N-6 independent internal
> >> coordinates (e.g., from a Z-matrix) and constrain all these bonds (by
> >> [constraints]), angles (by all-angles), and dihedrals (by adding 
> >> improper dihedrals with large force constants). Will this achieve a rigid
> >> molecule? Did anyone have any experience in this?
> >large force constants will make high-frequency vibration forcing you to
> >use very short time steps. Try adding long range constraints instead,
> >but be careful that it may be difficult to solve for the constraints
> >unless they are very accurately defined (distances). You may even need
> >double precision.
> >> 
> >> Thanks a lot for your help!
> >> 
> >> Lianqing
> >> 
> >> 
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> 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.
> >________________________________________________________________________
> >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
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the 
> >www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++