Dear Prof. Roitberg,
Thank you for your time and advise. You were right about the number of
ions. Now I am trying to fit the charges using RESP on AMBER.
Best regards
2015-08-20 12:41 GMT-04:00 Adrian Roitberg <roitberg.ufl.edu>:
> I am also confused as to why your TOTAL charge is not the same as the
> sum of H and G charges... Unless you are changing the number of ions,
> which would make it very hard to compute what you are trying to compute.
>
> adrian
>
>
> On 8/20/15 10:09 AM, Investigador Química wrote:
> > Dear Jason, thank you for your kind and clear explanation.
> > You are right. For the three isolated and solvated systems generated
> using
> > "solvateoct TIP3PBOX 11" we have:
> >
> > Box (x=y=z) triangulated 3-points waters sum of
> charges
> >
> > H-G 64,477 6598 -0.99950000
> > H 51,248 3254 -0.16460000
> > G 37,612 1321 -0.03280000
> >
> > My problem is how can I run the simulations with the water counts exactly
> > matched between the bound and unbound simulations?
> >
> > In AMBER tutorial 21 the following values are used for
> > water_tleap.in: solvatebox structure TIP3PBOX 16.50 iso
> > b2_tleap.in: solvatebox guest TIP3PBOX 13.16 iso
> > CB7_tleap.in: solvatebox host TIP3PBOX 10.18 iso
> > CB7_b2_tleap.in: solvatebox b2host TIP3PBOX 9.91 iso
> >
> > and manually they removed waters over 1500.
> >
> > In my case I do'nt know how to choose the appropriated number of waters
> or
> > the numbers of the
> > TIP3PBOX Nr? iso
> >
> > Could you please help me?
> >
> > Thank you for your help and time!
> >
> > Best regards
> >
> > 2015-08-19 11:18 GMT-04:00 Jason Swails <jason.swails.gmail.com>:
> >
> >> On Wed, 2015-08-19 at 10:43 -0400, Investigador Química wrote:
> >>> Dear Jason, thank you for your kind explanation. I recognize my first
> >>> question was not fortunate. Please let me to explain my question.
> >>> If I have the Etot for a host H, for a guest G and for the complex
> H-G, I
> >>> can calculate the interaction energy as E= E(complex H-G) - E(H) -
> E(G),
> >>> isn't?.
> >> Loosely speaking, yes. However, there are countless ways to do this
> >> wrong. For example, if the sum of the host and guest systems do not
> >> have exactly the same number (and *kind*) of atoms and molecules as the
> >> bound complex, then this energy difference is completely arbitrary (and
> >> meaningless). After all, energy is extensive, so you can tune the
> >> interaction energy to be any value you want by simply adding solvent to
> >> either the bound or unbound species and not to the other.
> >>
> >> There are many ways to compute the interaction energies (MM/PBSA is one
> >> example, and the linear response theory/linear interaction energy is
> >> another). Whichever you use must make sure that the only energies that
> >> are left after taking the difference are the interactions between the
> >> atoms in the host and the atoms in the guest.
> >>
> >>> If I get the energies for the three entities using solvateoct and
> >>> TIP3PBOX from 8 to 11 each time (for the three entities each time) I
> get
> >>> different interaction energies. Should the interaction energy best
> value
> >> be
> >>> the lower one?
> >> No. This is known as the variational principle and is common in QM
> >> calculations (i.e., a method is variational if a lower energy *ensures*
> >> a better approximation of the true wavefunction). Force fields are
> >> *certainly* not variational, and even variational QM Hamiltonians won't
> >> be variational in an interaction energy calculation like this.
> >>
> >>> How can I know that, if I have no experimental values to
> >>> compare with?
> >> You can't. You have to use your judgement and rationalize which model
> >> for computing the interaction energy is the best.
> >>
> >>> For instance these were the values I got when running 3 ns
> >>> of MD equilibration according to AMBER tutorial 1 section 5:
> >> 3 ns is a very short simulation.
> >>
> >>> box 8: E= -11067 kcal/mol
> >>> box 9: E= -10363 kcal/mol
> >>> box 10: E= -8276 kcal/mol
> >>> box 11: E= -6485 kcal/mol
> >> These are huge differences. You haven't described exactly how you are
> >> computing the interaction energies, but this looks to me like the fewer
> >> particles you use, the lower your energy gets. This can happen if you
> >> have 3 separate systems (H-G, H, G) each independently solvated and you
> >> take the energy of each one and subtract them. With an 11 A buffer, H+G
> >> will have a *lot* more water-water interactions between the two systems
> >> than the HG system compared with, say, an 8 A buffer. Which means that
> >> the total interaction energy will *appear* lower, because your
> >> difference includes more interactions than *just* those between your
> >> host and guest.
> >>
> >> Possible differences arising from box size effects will be related to
> >> periodic images interacting with each other, different conformational
> >> ensembles caused by either incomplete sampling or periodicity artifacts,
> >> and some net charge effects if you have a non-neutral unit cell with
> >> periodic boundary conditions. However, I wouldn't expect any of those
> >> effects (excluding incomplete sampling) to be larger than ~10 kcal/mol,
> >> let alone up to 5000!
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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>
--
Área de Software
Investigación Facultad de Química
Universidad de Santiago de Chile
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Received on Sat Aug 22 2015 - 14:00:06 PDT
