From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Fri Oct 20 2006 - 05:08:50 CDT
Molecular Dynamics of rigid body is a difficult problem.
In NAMD or in any MD program, you must "constraint" al 3N-6 freedom degrees.
This can be done with SHAKE (introducing set of costrained distance) or
increasing the constant force of all parameter. The second method is
catastrofic because you must define new set of integration time.....
If you want treat protein with body rigid approximation you can use ather MD
code like MOLDY.....
If you want can look this article
"A new algorithm for rigid body molecular dynamics"
N. Neto, L. Bellucci, Chemical Physics 328 (2006) 259-268.
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