AMBER Archive (2008)

Subject: Re: AMBER: D2O

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Mon Sep 15 2008 - 11:54:17 CDT

Dear Lin

Everyone has been trying to figure out if you are interested in D2O because:
a) the experimental is directly interested in and designed to measure
a property of the water in the system that is fundamentally based on
whether or not the water has deuterated protons
-or-
b) the experiment uses D2O for convenience (e.g. it is
spectroscopically distinguishable from H2O and in something like NMR,
it doesn't contribute to the proton signal) and ignores minor
thermodynamic and dynamic differences bewteen D2O and H2O

Since you have mentioned nothing about situation a), it seems like you
are in the situation b) and hence you just simulate with regular
(TIP3P, TIP4P-Ew, etc) water models !

I faced this same situation (see the reference below) and did just that.
I was measuring NMR relaxation times of alpha carbon position and
comparing to simulations. [We performed the measurement in D2O for
convenience and better signal since measuring in water would have
resulted in a far noisier signal due to overlap between the strong
water proton signal and the weak alpha proton signal.] We saw very
good prediction of even the dynamics of the D2O solvated peptide when
we solvated the simulated peptide in TIP4P-Ew water. We comment on
the difference between D2O and H2O and even do an extremely crude time
scaling (since at our temperature the D2O viscosity is 1.2 times that
or water) but the results do not change much. Of course, no empirical
water model is true water or true deuterated water so we don't expect
the match up to be perfect, but that was not the goal.

http://www.ncbi.nlm.nih.gov/pubmed/18412346
Fawzi NL, Phillips AH, Ruscio JZ, Doucleff M, Wemmer DE, Head-Gordon T.
Structure and dynamics of the Abeta(21-30) peptide from the interplay
of NMR experiments and molecular simulations.
J Am Chem Soc. 2008 May 14;130(19):6145-58. Epub 2008 Apr 16.

So, use H2O models and comment on any possible differences in
thermodynamic and dynamic properties. If you are interested in
dynamics, then TIP3P may not be the best choice since the dynamics are
much faster than H2O. David Case also has some recent work showing
TIP4P-Ew gives reasonable dynamics for proteins. But beware that
simulations with TIP4P-Ew will be slower, since it's more viscous and
it is more computationally expensive due to the fourth center in the
water.

Good luck
-Nick

On Thu, Sep 11, 2008 at 8:51 PM, Chih-Ying Lin <chihying_at_usc.edu> wrote:
>
>
> Hi
> The experiment observes the micelle in D2O solution.
> And. there is no other experiments done in H2O solution.
>
> and, I am going to simulate it..... and those are all I know.
> Lin
>
>
> ----- Original Message -----
> From: Adrian Roitberg <roitberg_at_qtp.ufl.edu>
> Date: Thursday, September 11, 2008 9:10 am
> Subject: Re: AMBER: D2O
> To: amber_at_scripps.edu
>
>> Let's see if I can help.
>>
>> Indeed, you 'can' use amber from a technical point of view. This
>> would
>> require a very slight amount of work, changing the mass of the H
>> atoms
>> in water in the prmtop from 1 to 2.
>>
>> This will give a very small different final density, but I do not
>> believe this would even be really measurable above errors bars.
>>
>> Besides that, I seriously question the 'need' or 'wisdom' in doing
>> such
>> simulations !
>>
>> If you are looking at H exchange from deuterated waters, NO
>> program will
>> help you unless you do the full calculation using fantastically
>> good
>> quantum mechanics and very long time scales. I do not believe
>> anyone has
>> done anything remotely like that for more than 5 or 6 water molecules.
>>
>> If you are looking at ANY other property, then it is unlikely
>> there
>> would ever be any difference between D2O and H2O, EVER.
>>
>> Let's think about this:
>>
>> 1. Under classical mechanics, the mass has NO effect on ANY
>> equilibrium
>> thermodynamic properties. The mass simply is nowhere to be found
>> in a
>> proper statistical description of a system.
>>
>> 2. Quantum mechanics only cares about masses when either a zero
>> point
>> energy needs to be computed, or tunneling happens. Since Amber
>> (and any
>> other classical MD program), for the most part, do not deal with
>> those
>> issues, D2O and H2O would behave EXACTLY the same for any
>> equilibrium
>> property. Exemptions are using PIMD for tunneling, etc, for those
>> are
>> for expert use.
>>
>> 3. Kinetics depends on masses in a non-trivial way. It has to do
>> with
>> the acceleration relating to mass and force, but then again, rates
>> for
>> reactions do not really depend on masses (see point 2 for caveats).
>>
>> To summarize, Amber is neither better not worse than any other
>> program
>> to do what you want to do, I seriously suggest that you tell us
>> exactly
>> what you think you can achieve by this simulation and maybe we can
>> help you.
>>
>> Adrian
>>
>>
>> Chih-Ying Lin wrote:
>> >
>> > I will simulate a system which the solutes embeded in the D2O
>> solution.>
>> > Am I suggested using Amber package to do so?
>> > or, no....
>> >
>> >
>> > Thank you
>> > Lin
>> >
>> > ----- Original Message -----
>> > From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> > Date: Tuesday, September 9, 2008 4:19 pm
>> > Subject: Re: AMBER: D2O
>> > To: amber_at_scripps.edu
>> >
>> >> but for what reason? what are you trying to learn?
>> >>
>> >> On Tue, Sep 9, 2008 at 3:59 PM, Chih-Ying Lin
>> <chihying_at_usc.edu>
>> >> wrote:>
>> >>> solute embeded in the D2O solution, instead of H2O solution
>> >>> what is the suggestion for this?
>> >>>
>> >>> ----- Original Message -----
>> >>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> >>> Date: Tuesday, September 9, 2008 11:21 am
>> >>> Subject: Re: AMBER: D2O
>> >>> To: amber_at_scripps.edu
>> >>>
>> >>>> it's important to first clarify to yourself and us what
>> >> properties of
>> >>>> D2O you are trying to reproduce, as compared to H2O. for
>> >> example, are
>> >>>> you looking at H/D exchange rates in NMR, or perhaps
>> enzymatic
>> >> KIE, or
>> >>>> something else? each of these would require a different
>> approach
>> >> (if>> they are even tractable at all)
>> >>>> On Tue, Sep 9, 2008 at 1:00 PM, Chih-Ying Lin <chihying_at_usc.edu>
>> >>>> wrote:>
>> >>>>> Hi
>> >>>>> Does amber support D2O simulation?
>> >>>>> What is the difference between H2O simulation and D2O
>> simulation?>>>>>
>> >>>>> And, how about the force field paramters of D2O?
>> >>>>>
>> >>>>> How to simulate the D2O system instead of H2O?
>> >>>>>
>> >>>>> Thank you
>> >>>>> Lin
>> >>>>> -------------------------------------------------------------
>> --
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>> >>>> -----
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>> >>
>> >> --
>> >> ===================================================================
>> >> Carlos L. Simmerling, Ph.D.
>> >> Associate Professor Phone: (631) 632-1336
>> >> Center for Structural Biology Fax: (631) 632-1555
>> >> CMM Bldg, Room G80
>> >> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>> >> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> >> ===================================================================
>> >> ----------------------------------------------------------------
>> ----
>> >> ---
>> >> The AMBER Mail Reflector
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>> ------
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>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>>
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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