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Hello Matthias-- > I wanted to submit the below to the xplor-nih listserver but got > rejected. you must be a member of the mailing list to be able to post a message- this avoids large amounts of spam on the list. > > with reference to your response "New kind of dynamic ?" > > of JUn.25, 2004 - maybe I have run into the following issue: > > We are trying to do refinement in explicit solvent following > > the method of Nilges and Linge but want to keep as many > > restraints as possible incl RCDs. It seems explicit solvent > > requires cartesian dynamics and the RCD code requires > > internal/dihedral angle dynamics. actually, neither of those statements is strictly true: explicit solvent calculations can be performed using internal coordinates. The water internal degrees of freedom can be frozen, and torsion angles used in the protein. On the other hand, RDCs can be included with cartesian dynamics- one must just be very careful. > Could you elaborate what > > you mean by "dynamics verlet is still the most efficient, but it > > is not generally approprite to use this integrator if pseudo atoms > > are present". Any ideas? It is more efficient to perform Cartesian dynamics using XPLOR's DYNAmics VERLet statement, than using the IVM, but I don't think the performance penalty is significant any longer. I am (slowly) working on a script to perform explicit solvent refinement using the IVM (easily including RDCs), but it's still at the pre-release stage. Have you tried refining using the database potentials? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFD9KTlPK2zrJwS/lYRAlbpAJ9+P51bl0iEuY2loL7l9vrsyOsQSACeMY0Z NNV1fKzIRbhiWMvF5XJyhiw= =1n8f -----END PGP SIGNATURE-----
