<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Cara,</span></div><div><span> Thanks for a very clarifying email. It helps a lot.</span></div><div>Sanku</div><div><br></div><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><font size="2" face="Arial"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Cara Kreck <cara_a_k@hotmail.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Friday, October 28, 2011 3:50 AM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] query on OPLS-2005<br></font><br>
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<div dir="ltr">Hi Sanku<br><br>According to the Schrodinger Knowledge Base, this is the paper that should be referenced for OPLS-2005 instead:<br>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)<br>(http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full)<br><br>The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br><br>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:<br>"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).<br><br>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.<br><br>Cara<br><br><br><br><div><hr id="yiv903241426stopSpelling">Date: Wed, 26 Oct 2011 15:02:07 -0700<br>From: msanku65@yahoo.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] query on OPLS-2005<br><br><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div>Hi,</div><div> 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?</div><div>So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. Is it also so-called OPLS-2005 forcefield?</div><div>Sanku</div></div><br>--
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