On 11/10/12 7:09 AM, Ali Alizadeh wrote:
Dear Rama
Thank you for your reply dear Rama,
I'm really sorry,
My link was wrong,
This link is correct:
cinjweb.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf
Of course this tutorial do not use opls-aa but it says some of
parameters about opls ff .(page-4)
I have no idea where these parameters come from (even the ones in Berk's notes).
I have never seen people use such settings with Gromos96, and those listed in
the table conflict with the protocols in the Gromos96 literature. Settings for
OPLS-AA are less clear. It is very common to use 1.0-nm cutoffs (and in fact
was the case in the Gromacs 4 paper), though the original OPLS literature used
different cutoffs depending upon what types of molecules were present, which is
not possible in Gromacs. You should read lots of papers by people who use
OPLS-AA for similar types of systems and evaluate their success or inaccuracies.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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