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 <ostue...@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 <ahmedo...@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 <ahmedo...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet Yıldırım
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