Dear all,
I would like to hear some thoughts on the use of the new Li & Mertz ion
parameters for protein-nucleic acids simulations. In particular I would
like to know from your experience, whether the 12-6-4 set is really
necessary for monovalent ions or whether either of the 12-6 sets (HFE
and IOD) are still reasonable choices for typical simulations with
neutralizing ions and some 150 mM additional salt .
Did anyone compare these parameters with the Smith&Dang parameters ?
Did anyone use the 12-6-4 set in NAMD ? Is NAMD able to read the
additional lines necessary in the AMBER topology files ?
Thanks for any insights ..
Best wishes
Vlad
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 12 2016 - 10:00:02 PST
