[gmx-users] rigid body again
lzheng at me.rochester.edu
Thu Jun 9 16:35:47 CEST 2005
Thanks, David! What is long range constraint? For an i-j-k-l dihedral,
try to constrain i---l distance?
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
>> Thanks a lot for your help!
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>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
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