[gmx-users] CHARMM ff cutoffs
Smith, Micholas D.
smithmd at ornl.gov
Thu Oct 19 16:33:27 CEST 2017
If you use the CHARMM-GUI (charmm-gui.org) to build your systems, they set their "standard" cut-offs to be 1.2nm, unless there is a membrane, then they set it to 1.4nm (at least that's what it use to do).
Changing cut-offs is kind of a mess. A lot of people will argue that the cut-offs are explicitly part of the force-field, and so whatever cut-offs were used for the parameterization are what you absolutely must use. But then you'll find papers (lake you did) that uses 0.95nm cut-offs and get reasonable results.
I would stick to the standard unless you have a really good reason (not performance) for toying with the cut-offs.
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of João Henriques <joao.m.a.henriques at gmail.com>
Sent: Thursday, October 19, 2017 10:03 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] CHARMM ff cutoffs
Is there any piece of literature that explicitly states what is the *de
facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic
interactions? The old gromacs site states it's 1.2 nm:
However, I've read Robert Best's C36 and Huang's C36m papers, along with
older CHARMM ff publications by MacKerell and Co., and I'm rather confused
at this point. E.g., on the C36m paper, the RS peptide is simulated with
0.95 nm cutoffs and other proteins with 1.2 nm. Robert is consistent and
uses 1.2 nm all the way. Older publications use even shorter cutoffs.
I know the cutoffs can probably be toyed with to a certain extent (Stefano
Piana and Kresten Lindorff-Larsen showed that on their 2012 paper), but a
recent paper by Davide Mercadante on JCTC seems to show that it is not so
simple for IDPs, and shortening the cutoffs is a no-no (even though he did
it for his KBFF and AMBER FFs, not CHARMM).
In my work I use CHARMM36m with 1.2 nm, but, looking at the literature,
there's no way I can justify my choice when the original C36m does not
stick to a single cutoff selection...
I know Justin is/was affiliated with the MacKerell lab, so maybe he can
shed some light on this subject. Anyone else is encouraged to give their
input as well.
Thank you in advance,
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