[gmx-users] CHARMM ff cutoffs

[João Henriques]

Dear Justin and Micholas,

First of all, I'd like thank both of you for the input. Greatly appreciated.

@Justin - I do agree with you and I understand why they might have done so
(performance-wise). Furthermore, until Davide's paper, and in light of
Stefano and Kresten's paper on the whole cutoff issue, it was more or less
assumed that something like 0.95 nm would be fine. The problem is that this
paper is special, since it is the official publication of the modification
to the C36 FF. Coherence should have been preserved, at least in my
personal opinion. In any case, I will do like you said and hand out your
name and url to the referee :) Just kidding, this isn't something I've been
asked (yet), but from experience, I have a feeling it will be a topic of
discussion. Plus, even if it isn't asked of me, I still want to have it
well justified in the paper.

@Micholas - Your argument would apply in most circumstances, but the
situation here is a bit more hairy for several reasons... which I am not at
liberty to discuss in public. I hope you understand.

Once again thank you for your input,
Best regards,
J


On Thu, Oct 19, 2017 at 4:54 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> 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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