Hi Barış ,
Thank you for responding.
That sounds more like periodicity (PN) you are talking about.
I have already assigned extra PNs as negative.
My question was rather about negative Vn/2/x values.
Best,
Cenk
On Mon, Feb 14, 2022 at 12:23 PM Barış KURT <peacewolfus09.gmail.com> wrote:
> Dear Cenk,
> negative value means there are more than one dihedrals... and divide 6
> means two atoms sees each other 6 times when you rotate them (360). In
> amber manual this subject explained in details. By the way, sometimes you
> will need a novel atom types (if you are not using gaff/gaff2). Please see
> my articles ...
> Regards,
>
>
> Cenk Andac <cenkandac.gmail.com>, 14 Şub 2022 Pzt, 12:10 tarihinde şunu
> yazdı:
>
> > Dear Prof. Simmerling,
> >
> > Thank you for your response and indispensible info you provided.
> >
> > IDIVF PK/6 PHASE PN
> > > > O-CT-N-C 1 0.382890 108.00 -1.
> > > >
> > >
> > > >it's not clear to me why you're dividing by 6.
> > >
> >
> >
> > > >(such as forgetting the factor of 2 in the amplitude, or getting the
> > units
> > > wrong,
> >
> >
> > Well, I have thought PK would equal to half the potential energy at the
> > energy barrier [PK=(V2)/2]. That is
> > indeed what I did. PK/6 indeed means (V2)/2/6 as I have stated that in
> my
> > previous message as follows
> > "Instead, I took half the max potential-energies at the barriers and
> > divided them by 6".
> > I guess, I should have formulated my statement before for clarification ,
> > PK=(V2)/2.
> > Overall, I actually divided the potential energy at the barrier by 12
> (V2 /
> > 12).
> > Sorry for keeping you in dark for not providing the real equilibration I
> > used.
> >
> > Is that what you were wondering? I would appreciate it much if you could
> > confirm the equilibration above?
> >
> > > a negative amplitude here just inverts that term in the Fourier series,
> > >with a minimum instead of maximum.
> >
> > That sounds interesting. I am currently doing a production run simulation
> > with the current parameters I found.
> > But, I also would like to try inverting the Fourier series for a minimum.
> > I am kind of in dark here though as I have not tried that before.
> > What do you mean exactly by "with a minimum"? Would that be the minimum
> > points right around the maximum point at the barrier ?
> > How would one invert the Fourier series?
> >
> > >you might look at some of the papers, such as for the mdgx program, or
> > paramfit, or our paper
> > >on ff14sb (ff19sb is more complicated since it's 2D parameters).
> >
> > I have looked at the ff19sb paper of yours. Well, that looks quite
> > advanced. Optimization of parameters
> > using a GRID model is quite interesting. It would be nice to learn that
> > algorithm for force field development.
> > How did you actually generate the GRIDs , using cpptraj or GAMESS-US?
> >
> > Regards,
> >
> > Cenk Andac
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Feb 8, 2022 at 12:55 AM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > I'll try to give you my thoughts on this, though there are many methods
> > in
> > > use.
> > >
> > > IDIVF PK/6 PHASE PN
> > > > O-CT-N-C 1 0.382890 108.00 -1.
> > > >
> > >
> > > it's not clear to me why you're dividing by 6.
> > >
> >
> >
> > > (such as forgetting the factor of 2 in the amplitude, or getting the
> > units
> > > wrong,
> > >
> > > > 1) It has been more than 10 years since I last parameterized a
> torsion
> > > > angle right. To refresh my memory, Can an amber expert possibly
> confirm
> > > the
> > > > general steps (outlined above) I took to derive the dihedral
> > parameters.
> > > >
> > >
> > > it seems reasonable, but there are many ways to do this. You might look
> > at
> > > some of the papers, such as for the mdgx program, or paramfit, or our
> > paper
> > > on ff14sb (ff19sb is more complicated since it's 2D parameters).
> > >
> > > >
> > > > 2) In line of PN = -3, PHASE = -250.41, a negative PHASE value, does
> > not
> > > > sound right to me? Can it be replaced with (360 - 250.41 =) 109.59 ?
> > > >
> > >
> > > the phase is just a shift in the position of the minimum and it
> shouldn't
> > > matter if you add 360 deg.
> > >
> > >
> > > > 3) I have checked some amber FF parameters and I noticed some
> negative
> > PK
> > > > values. What is the rationale for negative PK values as energy
> barriers
> > > > possess positive energies in difference PES curves after zeroing the
> > > lowest
> > > > minimum energy point?
> > > >
> > > > a negative amplitude here just inverts that term in the Fourier
> series,
> > > with a minimum instead of maximum. This could be done to reduce a
> barrier
> > > that is too large. The same can be achieved with a different phase, so
> > the
> > > details will depend on how the fitting was done. The rationale can vary
> > > depending on the protocol, but zeroing the lowest point isn't the only
> > way
> > > to approach the fitting, so it doesn't always work as you outlined
> above.
> > >
> > > I would suggest redoing your grid scan to get energies using your new
> > > parameters, and then making sure that the resulting energy profile is
> an
> > > accurate match to your target profile. There are many ways it can go
> > wrong
> > > (such as forgetting the factor of 2 in the amplitude, or getting the
> > units
> > > wrong, or getting the divider wrong when you have multiple terms
> > > contributing to the bond rotational energy, or other details of the
> > > dihedral equation).
> > >
> > > Thanks in advance for enlightening me.
> > > >
> > > > Best,
> > > >
> > > > Cenk Andac
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Received on Mon Feb 14 2022 - 07:30:03 PST
