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)?
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). 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?
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?
In that file, I see the subroutine get_nb_list. Furthermore, it seems
that QM-QM atom interactions are excluded in the subroutine pack_nb_list
(from line 1576 in nonbond_list.f, and then later also in
pack_nb_nogrdptrs):
if ( qmmm_nml%ifqnt ) then
if ( qmmm_struct%atom_mask(i) ) then ! then current atom is a QM atom
! skip interaction with all other QM atoms:
do qm_temp_count2=1, qmmm_struct%nquant
exclude(qmmm_nml%iqmatoms(qm_temp_count2))=i
end do
end if
end if
Maybe the way to go would be to do something similar, e.g. introduce a loop
that checks if both atoms i and j are of type A,B, and if so, exclude them.
Anyway, many thanks for your inputs, and any more feedback is welcome!
Marc
On 12 October 2011 01:59, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Oct 11, 2011 at 4:42 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > Hi all,
> >
> > For a future project, I am thinking of using hypothetical particles (with
> a
> > VdW radius and partial charge) that interact with a solute, but NOT (or
> > perhaps very little) with each other. The particles would have their own
> > atom types.
> > I don't think this would be possible without changing the code (i.e. by
> > hacking the prmtop or so), but please chime in if this is not the case.
> >
>
> The exclusion list will only allow you to omit non-bonded interactions
> between those atoms. If this is what you want to do, then editing the
> exclusion list should suffice. However, this requires an understanding of
> the topology file and knowledge of how to modify it properly (and how the
> exclusion list is constructed specifically in this case).
>
> I've actually written a topology file editing program specifically designed
> to make hacking the topology file easier that has the ability to modify the
> exclusion list in the way you describe. I'm hoping this will be released
> with the next version of AmberTools some time early next year.
>
>
> >
> > [snip]
> >
> > To start, I probably won't try using PME as this may make things more
> > complicated. I also don't care too much about affecting performance at
> this
> > stage.
> > As I am pretty much a novice when it comes to the AMBER code, it would be
> > great if someone could point me to where I could think of making changes.
> > Also, any ideas about different ways of doing this will be highly
> > appreciated.
> >
>
> True... If you wanted to use PME, then the exclusion list approach wouldn't
> work. The exclusion list only applies to the primary cell (or the
> direct-space part), which means that your long-range electrostatics will
> include unwanted contributions from your mystery-particles from different
> periodic boxes.
>
> If you want to get this behavior across periodic boxes, you'd have to
> modify
> the sander source code itself to get the desired behavior.
>
> HTH,
> Jason
>
>
> >
> > BTW, I did find an old thread in the archive that has some relevance
> > (although not quite the same, as I do want full non-bonded interactions
> > between the particles and the solute), but that may well be outdated as
> it
> > is from 2004:
> > http://archive.ambermd.org/200404/0263.html
> >
>
> > Many thanks,
> > Marc
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Wed Oct 12 2011 - 06:30:04 PDT
