AMBER Archive (2008)

Subject: Re: AMBER: D2O

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Sep 11 2008 - 10:20:07 CDT

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
>>>>> ---------------------------------------------------------------
>> ---
>>>> -----
>>>>> The AMBER Mail Reflector
>>>>> To post, send mail to amber_at_scripps.edu
>>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
>>>> email)> to majordomo_at_scripps.edu
>>>> -----------------------------------------------------------------
>> ---
>>>> ---
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber_at_scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
>> email)>> to majordomo_at_scripps.edu
>>> ------------------------------------------------------------------
>> -----
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the
>> email)> to majordomo_at_scripps.edu
>>
>>
>> --
>> ===================================================================
>> 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
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
                            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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu