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

[Oliver Stueker]

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