Hi Marc,
I thought your particles were bonded. That's why I suggested set.f. If
your particles are not bonded, you don't have to worry about it then.
Actually, if your particles are not bonded, and you only need A-X and
B-X non-bonded interactions, I have another way in mind. You could
create a input file that contains only coordinates, charges and vdW
parameters of all your particles. And let Sander read this file and
build a non-bonded list between your particle and other atoms (i.e.
A-X and B-X list). Build this kind of list is easy and relatively
fast,
do i=1, yourParticle
do j=1, otherAtom
building list
end do
end do
And you don't need to worry about build dummy bonds in leap or
elsewhere. One tricky thing I can think of now in this way, however,
is vdW interaction. You may need another file containing vdW's
parameters for other atoms. Hope this helps.
Best,
Qiantao
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)?
>
> 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 - 07:30:05 PDT
