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
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Received on Thu Oct 13 2011 - 03:30:02 PDT
