[gmx-users] CHARMM ff cutoffs

[Smith, Micholas D.]

Fair enough. 

Consider this then: of the systems tested in the CHARMM36m publication; which one is closest to yours (sequence similarity, structure)? That would be one way to decide which cut-off would be appropriate. 

Alternatively, you could just run the simulation multiple times with multiple cut-offs and see which one corresponds closest with experimental knowledge (though this would be challenge for IDPs, unless there is a known set of metastable structures that get sampled).

-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-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 10:46 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] CHARMM ff cutoffs

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.

Thanks!
J



On Thu, Oct 19, 2017 at 4:33 PM, Smith, Micholas D. <smithmd at 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-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
>
> 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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