[gmx-users] Re: Neigborsearching, Electrostatics and vdw options

[ahmet yıldırım]

Hi,

*quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm)
and a smooth particle mesh Ewald algorithm for Coulomb interactions
(switching distance of 0.9 nm) were used.*

i.e.this means:

; NEIGHBORSEARCHING PARAMETERS
.....
rlist                     = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype           = PME
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                       = 1.4

Am I wrong?
A twin range cut-off for van der Waals (0.9/1.4 nm) means rlist/rvdw. isnt
it?*
*
Thanks in advance*

*
22 Mart 2012 01:32 tarihinde Oliver Stueker <ostueker at gmail.com> yazdı:

> Hi Ahmet,
>
> > Let's imagine a sphere(two concentric spheres):
> > radius of the inside small sphere=rvdw
> > radius of the big sphere=rcoulomb
> > distance between two of our nested spheres:rlist
> > is this approach correct?
>
> No. I suggest you read section 4.6.3 (and  probably also 4.6.2) in the
> Gromacs Manual.
> The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone
> for the fact that the
> neighbor-lists are only updated every nstlist steps (often nstlist = 5).
>
> Oliver
>
> 2012/3/21 ahmet yıldırım <ahmedo047 at gmail.com>:
> > Dear users,
> >
> > Berk Hess says:
> > [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced
> units
> > Mon Jul 16 14:17:12 CEST 2007
> >
> > There are three options in Gromacs.
> >
> > The option you want is rcoulomb < rlist and rvdw < rlist.
> > This works and gives the most accurate and also the most costly
> integration.
> >
> > A faster and very commonly used setting is: rlist=rcoulomb=rvdw.
> > With PME the Coulomb interactions are very small at the cut-off,
> > as are the LJ interactions.
> > So with a small sacrifice in integration accuracy one can gain a lot
> > of performance, also because analytical LJ is cheaper than tabulated.
> >
> > The last option is rcoulomb > rlist and/or rvdw > rlist.
> > Then the energies and forces beyond rlist are only updated every nslist
> > steps.
> > This gives less integration accuracy but can give a lot of "interaction"
> > accuracy
> > at a small computational cost.
> >
> > Justin A. Lemkul says:
> > [gmx-users] Twin-range cut-off
> > Tue Sep 13 01:25:28 CEST 2011
> >
> >
> > A twin-range cutoff just means that your short-range cutoffs aren't all
> the
> > same
> > value, such that they form two interaction zones.  Within the shortest,
> the
> > neighbor list is updated every step.  Between the shortest and longest
> > cutoffs,
> > the neighbor list is updated every nstlist steps.  For instance:
> >
> > rlist = 0.9
> > rcoulomb = 0.9
> > rvdw = 1.4
> >
> > are common settings for Gromos96 force fields (in conjunction with PME).
> > Thus
> > there are two interaction zones - the first is if two atoms (or charge
> > groups,
> > depending on the algorithm) are within 0.9 nm, and the second is if the
> two
> > interacting species are beyond 0.9 nm but within 1.4 nm of each other.
> >
> > rcoulomb: distance for Coulomb cut-off (nm)
> > rvdw:distance for LJ or Buckingham cut-off (nm)
> > nstlist: neighbor list update frequency
> > rlist: cut-off distance of the short-range neighbor
> > Twin range cutoff consists of rcoulomb and rvdw, isnt it?
> >
> > Let's imagine a sphere(two concentric spheres):
> > radius of the inside small sphere=rvdw
> > radius of the big sphere=rcoulomb
> > distance between two of our nested spheres:rlist
> > is this approach correct?
> > I could not understand the fourierspacing and rlist.
> >
> >
> > Thanks in advance
> >
> >
> >
> > 21 Mart 2012 20:53 tarihinde ahmet yıldırım <ahmedo047 at gmail.com> yazdı:
> >
> >> Dear users,
> >>
> >> I have two configuration as the following related to Neigborsearching,
> >> Electrostatics and vdw options. I checked the literature:
> >> Generally the rlist, rcoulomb and rvdw have used as the following.
> >> rlist=1
> >> rcoulomb=0.8
> >> rvdw=1.4
> >>
> >> Is there much difference between the following two options in the
> >> calculation/the results? Is there one significant difference between
> the two
> >> options. If yes, then what is it? What is relationship between rlist,
> >> nstlist and rvdw/rcoulomb?
> >>
> >> Furthermore,
> >> fourierspacing         = 0.16
> >> or
> >> fourierspacing         = 0.12
> >> difference between these two options?
> >>
> >> 1.choice
> >> .....
> >> ; NEIGHBORSEARCHING PARAMETERS
> >> nstlist                 = 5
> >> ns-type               = Grid
> >> pbc                    = xyz
> >> rlist                    = 1.0
> >>
> >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> coulombtype              = PME
> >> pme_order                = 4
> >> fourierspacing          = 0.16
> >> rcoulomb                 = 1.0
> >> vdw-type                 = Cut-off
> >> rvdw                       = 1.0
> >> ...
> >>
> >> 2.choice
> >> ..
> >> ; NEIGHBORSEARCHING PARAMETERS
> >> nstlist                  = 5
> >> ns-type                = Grid
> >> pbc                      = xyz
> >> rlist                     = 0.9
> >>
> >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> coulombtype           = PME
> >> pme_order              = 4
> >> fourierspacing         = 0.16
> >> rcoulomb                 = 0.9
> >> vdw-type                 = Cut-off
> >> rvdw                       = 1.4
> >> ...
> >>
> >> Thanks in advance
> >> --
> >> Ahmet Yıldırım
> >>
> >
> >
> >
> > --
> > Ahmet Yıldırım
> --
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-- 
Ahmet Yıldırım
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