[gmx-users] rlist, rcolumb, and rvdw
Mark Abraham
mark.j.abraham at gmail.com
Thu Jan 12 08:30:29 CET 2017
Hi,
No, you need to design it correctly in the first place. See eg
http://manual.gromacs.org/documentation/2016.1/user-guide/cutoff-schemes.html
Mark
On Thu, 12 Jan 2017 05:31 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:
> Hi Mark,
>
>
> If I am using the older version of gromacs with group cutoff, what do you
> mean by "you always want a buffer"? Do we have to do some extra step after
> md simulation?
>
>
> Regards
>
>
> Sukriti
>
> [
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>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N)
> | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
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>
>
>
> ________________________________
> 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: Thursday, January 12, 2017 3:17:36 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] rlist, rcolumb, and rvdw
>
> Hi,
>
> On Wed, Jan 11, 2017 at 8:11 PM Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
> > I found the discussion and the links inside very useful. Thanks!
> >
> > I agree with was discussed above. I should not mess around with cut-offs
> > :-)
> >
> > Regarding the main question on this post (Just for curiosity):
> > If one wish to use 0.8-0.1 (mess around :-) ), shall we change the rlist
> > and rcolumb to 0.1 as well?
> >
>
> Depends on the cutoff scheme, and the GROMACS version.
>
> a) you always want a buffer, but the Verlet scheme will take care of that
> for you
> b) before GROMACS 2016, in the Verlet scheme, rvdw must equal rcoulomb in
> the .mdp file
> c) in GROMACS 2016, you are free to choose rvdw != rcoulomb so long as both
> are less than rlist, so you can shoot yourself in whichever part of your
> anatomy seems to you most in need of ventilation. :-)
>
> Mark
>
> OR,
> > as far as rlist is bigger than rvdw and rcolumb, we are good to to
> (except
> > taking more computing time)
> >
> > Cheers
> >
> > On Wed, Jan 11, 2017 at 7:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 1/11/17 9:42 AM, Thomas Piggot wrote:
> > >
> > >> Well, IMHO, for a lipids only system I'd would actually change those
> to
> > >> use
> > >> rvdw-switch = 0.8. Not only is this consistent with the original
> > CHARMM36
> > >> lipids
> > >> publication but for DPPC/POPC (at least) produces better membrane
> > >> properties in
> > >> GROMACS.
> > >>
> > >> See https://github.com/NMRLipids/NmrLipidsCholXray/issues/4 and my
> > >> comments/results in the discussion for more details.
> > >>
> > >>
> > > Interesting discussion. Indeed, the 1.0/1.2 cutoff settings are
> > preferred
> > > for compatibility with everything in the CHARMM36 force field. In our
> > > hands, when we tested DPPC, 0.8/1.2 and 1.0/1.2 produced results in
> > > reasonable agreement (e.g. the CHARMM-GUI paper referenced several
> times
> > in
> > > that discussion) though compressibility increased with the shorter
> > > switching region. We tested 0.8/1.0 because everyone complains about
> the
> > > "long" cutoff required to use CHARMM :) If only everything were like
> > > AMBER, which uses 0.8...
> > >
> > > All of this should become moot as we work to refine the force field
> with
> > > the recently implemented dispersion PME. No promises on when that will
> > be
> > > done, of course.
> > >
> > > -Justin
> > >
> > >
> > > Cheers
> > >>
> > >> Tom
> > >>
> > >> On 11/01/17 12:51, Justin Lemkul wrote:
> > >>
> > >>>
> > >>>
> > >>> On 1/11/17 2:57 AM, Mark Abraham wrote:
> > >>>
> > >>>> Hi,
> > >>>>
> > >>>> Those ancient comments pertain only to the deprecated "group" cutoff
> > >>>> scheme. You should look at the extensive documentation of both
> schemes
> > >>>> in
> > >>>> the current reference manuals. Particularly vdw cutoffs are baked
> into
> > >>>> the
> > >>>> forcefield and should not be varied without extensive testing. See
> > >>>>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
> > >>>>
> > >>>>
> > >>> To emphasize, this is especially true for CHARMM lipid parameters, as
> > is
> > >>> the
> > >>> case here.
> > >>>
> > >>> Repeat after me: "I will not mess around with cutoffs for lipids." :)
> > >>>
> > >>> -Justin
> > >>>
> > >>> Mark
> > >>>>
> > >>>> On Wed, 11 Jan 2017 04:51 Mohsen Ramezanpour <
> > >>>> ramezanpour.mohsen at gmail.com>
> > >>>> wrote:
> > >>>>
> > >>>> Dear gromacs users,
> > >>>>>
> > >>>>> Reading through mailing list I found a nice discussion on the
> > relation
> > >>>>> between rlist, rcolumb, and rvdw:
> > >>>>>
> > >>>>> https://www.mail-archive.com/gmx-users@gromacs.org/msg08387.html
> > >>>>>
> > >>>>>
> > >>>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
> > >>>>> /2011-February/058507.html
> > >>>>>
> > >>>>>
> > >>>>> If I understood correctly,
> > >>>>>
> > >>>>> rcoulomb < rlist and rvdw < rlist is the most accurate way,
> > >>>>>
> > >>>>> and
> > >>>>> rlist=rcoulomb=rvdw is the commonly used way for these parameters.
> > >>>>>
> > >>>>> I was wondering what would be the case if I want to change the
> > >>>>> cut-offs?
> > >>>>>
> > >>>>> For instance, to use charmm36 in Groamcs, it is recommended to use
> > >>>>> 1.0-1.2
> > >>>>>
> > >>>>> as the cut-off for LJ, and rlist=rcoulomb=rvdw
> > >>>>>
> > >>>>> However, this setting might not result in good behaviour for some
> > >>>>> lipid bilayers.
> > >>>>>
> > >>>>> Therefore, I want to check if other cut-offs works better in
> gromacs.
> > >>>>>
> > >>>>> If I change "1.2 nm" to "A nm" for rvdw, do I need to change
> rcolumb
> > >>>>> and
> > >>>>> rlist to A as well? i.e. rlist=rcolumb=rvdw=A?
> > >>>>>
> > >>>>> I am using following parameters already:
> > >>>>>
> > >>>>> cutoff-scheme = Verlet
> > >>>>> nstlist = 20
> > >>>>> rlist = *1.2*
> > >>>>> coulombtype = *pme*
> > >>>>> rcoulomb = *1.2*
> > >>>>> vdwtype = Cut-off
> > >>>>> vdw-modifier = *Force-switch*
> > >>>>> rvdw_switch = *1.0*
> > >>>>> rvdw = *1.2*
> > >>>>>
> > >>>>> Thanks in advance for your comments
> > >>>>> Cheers
> > >>>>> Mohsen
> > >>>>> --
> > >>>>> *Rewards work better than punishment ...*
> > >>>>> --
> > >>>>> Gromacs Users mailing list
> > >>>>>
> > >>>>> * Please search the archive at
> > >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>>>> posting!
> > >>>>>
> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>
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> > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > >>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>
> > >>>>>
> > >>>
> > >>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > > --
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> >
> >
> >
> > --
> > *Rewards work better than punishment ...*
> > --
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