Hi Cara,
Thanks for a very clarifying email. It helps a lot.
Sanku
________________________________
From: Cara Kreck <cara_...@hotmail.com>
To: gmx-users@gromacs.org
Sent: Friday, October 28, 2011 3:50 AM
Subject: RE: [gmx-users] query on OPLS-2005
Hi Sanku
According to the Schrodinger Knowledge Base, this is the paper that should be
referenced for OPLS-2005 instead:
Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A.
Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y.
Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated
Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752
(2005)
(http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full)
The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field
(2001 aminoacid dihedrals)
OPLS-AA/L seems to presented in the above paper as their updated version, but
it is sourced from the 2001 paper on proteins which is listed as a reference in
the Gromacs oplsaa.ff/forcefield.itp file. The 2005 paper then adds the
following:
"New force-field parameters were developed for OPLS_2003 for organic
functional groups for which the OPLS_2001 force field does not provide
specific parameters. Previously derived parameters for proteins, discussed
above, were implemented without modification in OPLS_2003." (Where 2003
apparently evolved into 2005).
So it looks like the protein section of both force-fields are the same, but if
you want to use other parameters you should check them individually first to
see whether or not they were changed or created since 2001.
Cara
________________________________
Date: Wed, 26 Oct 2011 15:02:07 -0700
From: msank...@yahoo.com
To: gmx-users@gromacs.org
Subject: [gmx-users] query on OPLS-2005
Hi,
I wanted to check what is actually OPLS-2005 forcefield that is recently
being referred often for md simulation. However, I also see that whenever,
OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS
forcefield. So, what is actually OPLS-2005?
So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series.
Is it also so-called OPLS-2005 forcefield?
Sanku
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