>
> 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 b
Hi,
On Tue, Jan 23, 2018 at 6:27 PM Faezeh Pousaneh wrote:
> Hi Mark,
> thanks for remarks, just one point:
>
>
> > > 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 fo
Hi Mark,
thanks for remarks, just one point:
> > 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.
> >
>
> You're seeing the
Hi,
On Tue, Jan 23, 2018 at 1:31 PM Faezeh Pousaneh wrote:
> >
> >
> >
> > > 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).
> >
>
>
>
>
> > 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
> th
Hi,
On Mon, Jan 22, 2018 at 10:25 AM Faezeh Pousaneh
wrote:
> 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 d
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). From the resulted LJ potential
between two particles I see that it takes the potential to zero at rlist,
not
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 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
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
wrot
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 wrote:
> Dear Mark,
>
> Thank you, however, the problem occurs when 'table' is used. For
> vdWt
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
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.
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
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