Dear Ambers,
I have started studying the new features introduced in AMBER10 and I
observed the incorporation of the flexible water model SPCFW. I have
read the original paper about it and I am tempted to start some tests
with it in simulations without SHAKE.
Now I would like to ask you if somebody has started using this model and
if yes, are there any issues one should really take care of before using
it (beyond the time step issue). Second, if one wants to add lets say a
150 mM NaCl to a simulation with this water model, I assume none of the
ion parameters supplied with amber10 (including the new params from Tom
Cheatham's group) would be appropriate. Any comment or suggestion here ?
I assume one could apply the same scheme as Tom and S. Joung did to
derive ion parameters for this water model as well.
Are Tom's ion parameters already published? The Amber Tools manual says
"manuscript in preparation".
Thanks for any thoughts on this
Best wishes
vlad
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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Received on Wed Jun 18 2008 - 06:07:30 PDT
