On Thu, Oct 13, 2011 at 7:03 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
> **
>
> Hi Marc and Jason,
>
> thank you for bringing this up...
>
> I am also interested to run a system where non-bonded interaction are
> switched off especially VDW
>
> Electrostatics was turned off by reducing the partial charges to zero.
>
> I guess by altering this flag %FLAG EXCLUDED_ATOMS_LIST in the topology
> file both VDW + ELE will be turned off
>
> ps. if there is a script that can read and edit the topology file .. I
> would be interested to try it out
>
>From the sound of what you're doing, it doesn't seem like you even need to
alter the exclusion list. The only reason Marc has to do that is because he
wants his particles to interact with *some* atoms, but not others. If
reducing the partial atomic charges to 0 fits your needs (thereby
eliminating *all* nonbonded electrostatics interactions), then it also
sounds like you can change the VDW parameters on your non-interacting atoms
to 0 to turn off interactions between those atoms and everybody else.
You can either do this at the frcmod level before building the topology
files with leap, or the program I had been mentioning does this as well.
It's important to note the difference between modifying the exclusion list
and zero-ing the VDW and charge parameters, and analyze what you're really
trying to learn before picking a particular route.
HTH,
Jason
>
>
> regards
> Fatima
>
>
>
> -----Original Message-----
> From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com<marcvanderkamp.gmail.com>
> ]
> Sent: Thu 13/10/2011 11:17
> To: AMBER Mailing List
> Subject: Re: [AMBER] Turning off non-bonded interactions for
> specificatomtype pairs
>
> Hi Jason,
>
> Thanks again for your useful input.
> Before I saw your reply, I looked a bit more at the
> prmtop EXCLUDED_ATOMS_LIST and NUMBER_EXCLUDED_ATOMS sections, and got the
> feeling that I could do what I want to do by manipulating those.
> I am very glad you've confirmed this, and clarified these sections to me in
> the process.
>
> I'm obviously not interested in changing the code anymore, now I know
> changing the prmtop will suffice. (Also, creating "bonds" between the
> particles was only meant as a way to check that I'd get the correct atoms
> in
> the exclusion list, not really as a way to get this to work in practice.)
> But, as you rightly point out, changing the prmtop for this purpose isn't
> trivial. Your program, with the new code you've so kindly added, would be
> very useful in this respect!
>
> Thanks,
> Marc
>
> On 12 October 2011 18:27, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Wed, Oct 12, 2011 at 9:21 AM, Marc van der Kamp <
> > marcvanderkamp.gmail.com
> > > wrote:
> >
> > > Thanks Jason and Qiantao for your replies!
> > >
> > > To clarify, what I aim to do is to turn off non-bonded interactions
> > between
> > > certain particles, whilst maintaining non-bonded interactions between
> the
> > > particles and a solute.
> > > In other words, if my particle atom types are A and B and we call all
> > other
> > > atom types X, then I want to turn off these non-bonded
> > > interactions: A-A, A-B, B-B
> > > Whilst keeping: A-X, B-X
> > >
> > > Jason, is this really possible by 'just' modifying the topology? I
> > presume
> > > you mean hacking the %FLAG EXCLUDED_ATOMS_LIST section, or (also)
> > > elsewhere?
> > > Wouldn't I be turning off all non-bonded interactions for specific
> atoms
> > > (so
> > > also A-X and B-X)?
> > >
> >
> > Yes, it's possible by "just modifying the topology" (I keep the quotes to
> > imply that it's trivial in theory, but quite painful to do by hand to the
> > point of impossibility for large topology files). The excluded atoms
> list
> > effectively defines a list of atom pairs whose pairwise non-bonded
> > potentials will be excluded ("bonding" 2 atoms together tells leap to add
> > these two atoms to each others' exclusion list so their non-bonded
> > potential
> > will not be calculated). The section EXCLUDED_ATOMS_LIST is a long list
> > that is broken up into a list of atoms to be ignored for each atom.
> sander
> > knows which excluded atoms belong to which atoms (which part of the
> > EXCLUDED_ATOMS_LIST belongs to each atom) via the NUMBER_EXCLUDED_ATOMS
> > section, which effectively tells sander how many excluded atoms each atom
> > has.
> >
> >
> > >
> > > Re: using bonds between all A-A, A-B and B-B pairs:
> > > Jason, I was thinking of using one-atom particles, so creating angles
> and
> > > dihedrals by defining bonds between these shouldn't be a problem (as
> long
> > > as
> > > I define them, using zero force constants). My point was that, in order
> > to
> > > exclude interactions for all A-A, A-B and B-B pairs, I'd have to
> > introduce
> > > a
> > > lot of "bonds" (just as many as there are non-bonded evaluations in a
> > > system
> > > with infinite cut-off).
> >
> >
> > But this operates via the exclusion list that I had suggested modifying,
> > anyway. The excluded_atoms_list is just a list of atoms that form bonds,
> > angles, or dihedrals with each of the atoms in the system. The point
> that
> > I
> > was trying to make is that if these magical particles are bonded to any
> > *other* atom (not *just* to each other), then you will be modifying the
> > exclusion list more than you would expect. For instance, suppose mystery
> > particle X is bonded to atom A and mystery particle Y is bonded to atom
> B.
> > If you then create a bond between the mystery particles X and Y, A and B
> > have now formed a dihedral with one another and are therefore added to
> the
> > exclusion list, so their non-bonded interactions will not be calculated
> > normally (they'll be calculated and scaled according to the 1-4 scaling).
> > This is what I was talking about. Creating bonds is a simple way of
> > modifying the exclusion list, but it can have more effects than you
> > anticipate due to added angles and dihedrals as a result.
> >
> >
> > > So if the number of A and B particles is big, I
> > > would guess it would start hurting performance (even though a bond-term
> > > should take less time to evaluate than a Lennard-Jones 6-12 term). Or
> am
> > I
> > > missing something?
> > >
> >
> > This part scales as number of mystery particles ** 2, I think. Again,
> your
> > reason to create all of these bonds is just to add these atoms to the
> > exclusion list, so why not just do that directly (without having to
> > calculate all of these useless bonds, angles, and dihedrals)?
> >
> > Re: where to start in case I'd need to change code:
> > > Qiantao, you suggested looking at src/sander/set.f. But, as I'm dealing
> > > with
> > > changing non-bonded interactions, shouldn't that be
> > > src/sander/nonbond_list.f?
> > >
> >
> > This is just the non-bonded pairlist. You could certainly tinker with it
> > so
> > that mystery particles don't end up in each others' pair lists, but this
> > *only* affects the direct-space interactions for PME simulations (GB and
> > vacuum simulations don't have a pairlist, or I guess you could say every
> > atom has a full pairlist by virtue of not having an explicit one
> > allocated). Therefore, this approach won't work for GB simulations, and
> > will have the same effect as hacking the excluded atoms list for PME
> > simulations, unless I'm missing something here.
> >
> > Like I mentioned previously, I've written a topology file editor that
> makes
> > this kind of stuff easier. I took 5 minutes last night to explicitly add
> > the ability to modify exclusion lists the way you want, since it only
> > required ~20 additional lines of code to the program and was
> > straightforward
> > to do. If you want to give it a try, contact me off-list and we can try
> to
> > get it working.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 13 2011 - 06:00:02 PDT
