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From: Adrian Roitberg <roitberg.ufl.edu>

Date: Thu, 20 Aug 2015 12:41:52 -0400

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
*

*>>
*

*>
*

*>
*

Date: Thu, 20 Aug 2015 12:41:52 -0400

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:

-- Dr. Adrian E. Roitberg Professor. Department of Chemistry University of Florida roitberg.ufl.edu 352-392-6972 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 20 2015 - 10:00:04 PDT

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