On 10/19/17 10:46 AM, João Henriques wrote:
Dear Micholas,
First of all, thank you for your input. I understand the whole cutoff
problematic and it is my desire to stick to the standard. However (and
maybe I didn't explain this part properly), the CHARMM36m publication
reports different cutoffs (if you check the SI) depending on which protein
is simulated. This publication *IS* the standard, right? I am well aware
that other CHARMM implementations use 1.2 nm, but if you go further back in
time, the cutoffs have taken other values. But I digress, the main question
here is, how can I justify my choice when the official publication reports
these two values and does not provide an explanation for it? I am well
aware that the 1.2 nm value is the *de facto* value, but that is not an
acceptable justification in the eyes of a journal referee, as we all can
understand.
Disclaimer: I was not involved in designing the methods for the paper
you mention, so you may want to email Alex about it for absolute certainty.
But what I can say is that we understand that the protein and nucleic
acid force fields are more tolerant to changes in cutoff (as compared to
the lipids, for example, which turn into an absolute disaster when
changing things), so sometimes it is OK to reduce them especially in the
case of a huge system or big REMD job to speed things up. I generally DO
NOT advocate for this, because if you tell people you can toy with
cutoffs, they start doing it without understanding the underlying
physics or knowing how to check if things are actually OK.
If you want to be safe, use what I have posted on the GROMACS website.
That is what is used in 99.9% of all CHARMM protein and nucleic acid
simulations (at least, the good ones :). Lipid cutoffs can vary and
there's lots of literature about that (and some open debate - see work
by Jeff Klauda, Tom Piggot, etc).
As soon as the force fields are reparametrized for use with LJ-PME, this
whole debate will be rendered moot. In time...
-Justin
Thanks!
J
On Thu, Oct 19, 2017 at 4:33 PM, Smith, Micholas D. <smit...@ornl.gov>
wrote:
João,
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
===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
Henriques <joao.m.a.henriq...@gmail.com>
Sent: Thursday, October 19, 2017 10:03 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] CHARMM ff cutoffs
Dear all,
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:
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
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,
Best regards,
João
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==================================================
Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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