[gmx-users] rlist, rcolumb, and rvdw

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Thu Jan 12 05:31:01 CET 2017 

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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________________________________
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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
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>
>
>
> --
> *Rewards work better than punishment ...*
> --
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