[gmx-users] Gromos54a7 electrostatics interactions ?

[Sim gmx]

First of all, thanks for your replies!

1) Indeed, both epsilon-r and epsilon-rf are such constants. However, in
the paper I guess that they refer to the relative dielectric constant of
the reaction field, i.e. epsilon-rf. Or do I miss something ?

2) I will for sure contact them to collect all these info if I go further
with this forcefield!

3) I don't think I understand everything there. What I think I get is:
using a verlet scheme with parameters that were not initially designed for
this scheme is risky and should be carefully assessed. Plus, parameters
used by Poger are very likely to be incompatible with verlet scheme.
>From this, I conclude it's not even worth giving it a try. So my options
are:
- use a group scheme, that will be slower
- use a different force field, but which one since I do have the topologies
of my small molecules for gromos 53a6/54a7 ? Would Berger Lipids be a good
option here ?

About Tom's reply:

1. That's good to know, especially as it does not appear anywhere in the
original papers.
2. Is using a setup with all cutoffs = 1.4 more "adequate" than the
twin-range setup then ? Or is it just a "good to know" stuff ? I would
naturally use the fastest correct setup which seems to be the twin-range
one (with group-scheme), am I wrong ?

Again, thanks to both of you.

2017-09-22 14:29 GMT+02:00 Piggot T. <T.Piggot at soton.ac.uk>:

> Hi,
>
> In addition to Mark's comments, there are a few other points to be aware
> of:
>
> 1. If you use the twin-range scheme (i.e. 0.8/1.4) with nstlist 5, you
> need to set nstcalclr to 1 to get results matching those as reported by
> Poger and co-workers (see http://pubs.acs.org/doi/abs/
> 10.1021/acs.jctc.7b00178?src=recsys). This is the fastest setup that will
> give you the 'correct' membrane properties with the group scheme.
>
> 2. The combination of reaction field with Verlet and all cutoffs set to
> 1.4 does not give the correct membrane properties for DPPC (these are my
> own results). Using the group scheme with this setup is fine but slower
> than the twin-range setup mentioned above. You should therefore use the
> group setup if using reaction-field with this force field. If you wish to
> use PME the membrane will be more ordered. However, Verlet and group
> schemes give the same results for PME (again my results),
>
> Regarding the second point, can anyone shed some more light onto why using
> the Verlet scheme would result in substantially different membrane
> properties to the group scheme with a single 1.4 nm cutoff and
> reaction-field (PME gives the same membrane properties using these two
> setups)?
>
> Cheers
>
> Tom
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: 22 September 2017 12:41
> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Gromos54a7 electrostatics interactions ?
>
> Hi,
>
> On Fri, Sep 22, 2017 at 10:21 AM Sim gmx <simgmx at gmail.com> wrote:
>
> > Hi!
> >
> > I would like to do simulations of lipids bilayers with gromos54a7
> > parameters. To do so, I want to use the same mdp parameters as Poger et
> al.
> > (the authors).
> >
> > In their papers, they write : "Nonbonded interactions were evaluated
> using
> > a twin-range cutoff scheme: interactions falling within the 0.8-nm
> > short-range cutoff were calculated every step, whereas interactions
> falling
> > within the 1.4-nm long-range cutoff were updated every 10 fs, together
> with
> > the pair list. A reaction-field correction was applied to account for the
> > truncation of the electrostatic interactions beyond the long-range cutoff
> > using a relative dielectric permittivity constant of 62, as appropriate
> for
> > SPC water"
> >
>
> Note that such twin-range multiple stepping schemes have only ever been
> supported in GROMACS in the group cutoff scheme, and not at all in the most
> recent versions. See (older versions of) the reference manual for
> discussion of known issues with the twin-range scheme. However, parameters
> derived with this irreversible (and thus unphysical) scheme have usually
> been shown to be usable outside that scheme, but obviously there's a higher
> burden of validation bourne by a the user in that case.
>
> From this, I conclude that my mdp file should contain something like (among
> > other parameters):
> >
> > dt=0.002
> > vdw-type = cut-off
> > rlist = 0.8
> > nstlist = 5
> > rvdw = 1.4
> > coulombtype = reaction-field
> > epsilon-rf = 62
> >
> > My questions are:
> >
> > 1) Does "relative dielectric permittivity constant" indeed mean
> > "epsilon-rf" here (not epsilon-r) ?
> >
>
> That's not the right question, both epsilon and epsilon-rf are such
> constants. See
> http://manual.gromacs.org/documentation/2016.4/user-
> guide/mdp-options.html#electrostatics
> for
> the different parts of the coulomb contributions to which they refer.
>
>
> > 2) What about the coulomb cut-off (rcoulomb) ? I think that in
> gromos53a6,
> > rcoulomb is often set to 0.9 (here I guess it would be 0.8 to match the
> > rlist). However, if the reaction-field correction is applied "to account
> > for the truncation of the electrostatic interactions beyond *the
> long-range
> > cutoff*", I would set rcoulomb to 1.4. As no explicit reference to
> rcoulomb
> > is done in the papers, I fear to miss something here.
> >
>
> They refer to non-bonded interactions, that means both Coulomb and VDW.
> Your interpretation is correct for the group scheme. Their text implies
> rlist=0.8 and the others 1.4. You should also ask them if they used GROMACS
> and to supply a sample .mdp file so you can reproduce their reported
> results.
>
> 3) If rcoulomb has indeed to be set to 1.4 as rvdw, it becomes possible to
> > use a verlet cut-off scheme to benefit from GPU acceleration. However,
> when
> > verlet cut-off scheme is used, mdrun shifts the nstlist and rlist to
> higher
> > values. Isn't it likely to impact the simulation reliability in such
> cases
> > ?
> >
>
> Be careful with terms here. *Reliability* is whether the combination of
> code and force field correctly reproduces the results for which it was
> parameterized. Since you cannot use the twin-range implementation of the
> group scheme in the Verlet scheme, you will be using a different setup. You
> should absolutely evaluate reliability yourself - can you reproduce the
> experimental observables that the parameterization claims, and do they
> accompany plausible values for the observables in which you are interested?
> The Verlet scheme uses and interprets rlist differently (and if we had our
> decisions over again, we should not have been re-using rlist and nstlist
> for schemes with rather different behaviour).
>
> The question of which setup is more likely to produce a useful physical
> model for given computational cost is open, but consensus in the field
> suggests that the features of
>
> a) symplectic integration (which implies reversibility),
> b) suitable conservation of a quantity (thus adequate buffering),
> c) explicit handling of non-isotropic long-range effects (including at
> least electrostatic, but preferably also dispersion PME)
>
> are highly desirable (particulary if the system is not isotropic).
> Unfortunately the scheme that Poger used in their parameterization has none
> of those properties.
>
> Mark
>
>
> > Thank you in advance for your replies!
> > --
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