> > > > > For any range of cut off it gives wrong results for rlist>rcut-off. > > > > Now I understand where the problem comes. I tried to see the collisions > of > > two molecules with a table (user potential). > > > Over what range is your interaction defined? If the potential isn't zero by > the time you get to the relevant cutoff, then you will produce artefacts. > > > I use same 6,12 table in Gromacs top folder, which goes to 1+rc.
> > From the resulted LJ potential > > between two particles I see that it takes the potential to zero at rlist, > > not at rcut-off. > > how to deal with it now? > > > > If the interaction isn't in the list, it doesn't get computed. > > I hope you got my point. I assume when I define rcut-off in .mdp file, the resulted potential should be zero after this value, so the larger rlist > rcut-off wont make difference. But what I see from resulted potential vs displacement of two molecules, is that Gromacs has taken the potential to zero at rlist not *''rcut-off''*. That is why for rcut-off > rlist the result is not correct. So the solution for me now is to put the potential in the table file to zero manually for x>cut-off. But it is better to solve the problem in Gromacs. > 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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