> > Hi again, >
> Yes. But I thought your comment was referring to "taking the potential to > zero." Neither the cutoff implementation nor your table was doing that at > rcutoff, so any particle in the list got computed regardless of rcutoff. > When you saw a zero-strength interaction, that was because the particles > weren't being put in the list, and not because it was in the list and > evaluated as zero strength. > > Mark, I thinks there has been misunderstanding. I never saw zero interactions. What I mean is: with a LJ table 6,12 given in Gromacs page (even my own other user tables), when I take rlist=0.6 and rvdw=0.5 in .mdp file, the resulted potential from simulation shows that instead of potential becomes zero at rvdW=0.5, it gets zero at rlist=0.6. So many unwanted interactions are counted. Which is an important point to know about Gromacs fails here. It is OK as long as rvdw-off=rcoulmb=rlist. But if we have a case with rvdW<rcoulomb, it fails. That is why, in order to avoid that I should change the table manually to insert rvdW smoothly to zero. > Mark > > > So the solution for me now is to put the potential in the table file to > > > > zero manually for x>cut-off. > > > > > > > > > Glancing at the kernels that implement user tables, that's what you > > should > > > do. That means the forces are strange and you would wish to consider a > > form > > > where the potential smoothly reaches zero at the cutoff. > > > > > > But it is better to solve the problem in > > > > Gromacs. > > > > > > > > > > It looks like the group scheme with user tables doesn't have support > for > > > buffered lists with a correct cutoff. That correct cutoff is only > > available > > > in the group scheme for potentials that do go to zero. Likely we > > concluded > > > that because you have the ability to express your wishes entirely in > your > > > table, you should do so. Or use rlist == rvdw == rcoulomb. > > > > > > Mark > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > > > > > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham < > > > > mark.j.abra...@gmail.com > > > > > > > > > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > Yes, you said that before. But I asked what range it worked > over, > > > ie > > > > > what > > > > > > > range of cutoff. > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh < > fpoosa...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > > > > > Hi Mark, > > > > > > > > > > > > > > > > For rlist=rcut-off (max one) it works correctly, but as soon > as > > > > > rlist> > > > > > > > > rcut-off it fails and gives different energies. Which I do > not > > > > > > understand > > > > > > > > why. In principle, there is nothing going on after cut-off in > > > > > > potentials. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > > > > > > > > > > > > > On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham < > > > > > > mark.j.abra...@gmail.com> > > > > > > > > wrote: > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > There could be. But over what range does your table work > > > > correctly? > > > > > > > What > > > > > > > > do > > > > > > > > > you get when you have a two particle system at various > > > > > displacements? > > > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh < > > > fpoosa...@gmail.com > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > Dear Mark, > > > > > > > > > > > > > > > > > > > > Thank you, however, the problem occurs when 'table' is > > used. > > > > For > > > > > > > > > > vdWtype=not-user the energies are OK and the same for > both > > > > cases, > > > > > > as > > > > > > > I > > > > > > > > > > mentioned. So I guess there should be something wrong in > > the > > > > way > > > > > > > > Gromacs > > > > > > > > > > interpolates the table with cutoffs and rlist. > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham < > > > > > > > > mark.j.abra...@gmail.com> > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > > > > > With the group scheme, when you choose nstlist > 1 then > > you > > > > > get a > > > > > > > > list > > > > > > > > > of > > > > > > > > > > > all the groups that satisfy rlist, whatever it is, and > > > > continue > > > > > > to > > > > > > > > use > > > > > > > > > > that > > > > > > > > > > > list for the whole lifetime. If you chose > > rlist==rcoulomb, > > > > then > > > > > > > > > rcoulomb > > > > > > > > > > is > > > > > > > > > > > never considered again, because you chose to use an > > > > unbuffered > > > > > > > list. > > > > > > > > > But > > > > > > > > > > > with rlist > rcoulomb, you chose the list to have > > > > interactions > > > > > > that > > > > > > > > are > > > > > > > > > > not > > > > > > > > > > > within rcoulomb, so every interaction is checked at > every > > > > step > > > > > > for > > > > > > > > > > whether > > > > > > > > > > > it is within rcoulomb, before including it. That's > slower > > > to > > > > > run, > > > > > > > > but a > > > > > > > > > > > better approach. And of course you can't expect them to > > > > compute > > > > > > the > > > > > > > > > same > > > > > > > > > > > numbers, particularly if things move fast relative to > the > > > > > buffer > > > > > > > size > > > > > > > > > and > > > > > > > > > > > list lifetime. > > > > > > > > > > > > > > > > > > > > > > The Verlet scheme defaults do a good job of automating > > all > > > > > this, > > > > > > > but > > > > > > > > as > > > > > > > > > > you > > > > > > > > > > > know, there's not yet support for tabulated > interactions. > > > > > > > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > > On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh < > > > > > fpoosa...@gmail.com > > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > > > > > > > I run a simple example using Table,6,12 (for LJ) with > > vdW > > > > > type= > > > > > > > > user. > > > > > > > > > > > Then > > > > > > > > > > > > group scheme should be chosen. > > > > > > > > > > > > > > > > > > > > > > > > In results, I got different LJ energies when I set > > > > > > rlist=rcoulomb > > > > > > > > and > > > > > > > > > > > > rlist>rcoulomb (which is allowed in this scheme). I > see > > > in > > > > > the > > > > > > > > manual > > > > > > > > > > > that > > > > > > > > > > > > with group scheme that can be happen. But I do not > find > > > how > > > > > to > > > > > > > get > > > > > > > > > rid > > > > > > > > > > of > > > > > > > > > > > > the differences in energies? or which rlist is the > > case. > > > > > > > > > > > > > > > > > > > > > > > > However, when I run with vdW type= cutoff for both > > rlist > > > > > > > > > > rlist=rcoulomb > > > > > > > > > > > > and rlist>rcoulomb with group scheme I get similar > > > results. > > > > > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > -- > > > > > > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > > > > > before > > > > > > > > > > > > posting! > > > > > > > > > > > > > > > > > > > > > > > > * Can't post? 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