I'm sorry but we can't seem to help you. I've tried to explain that
the method you need to use and therefore whether it is possible or not
in Amber depends on what you are trying to learn from the simulation.
This is true for almost every simulation- the method you use depends
on the data you want to obtain. All simulations involve a choice of
approximations, and the choice you make depends on the data that you
want. If you can't tell us this, we can't help you.
good luck!
On Thu, Sep 11, 2008 at 10:32 AM, Chih-Ying Lin <chihying.usc.edu> 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.gmail.com>
> Date: Tuesday, September 9, 2008 4:19 pm
> Subject: Re: AMBER: D2O
> To: amber.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.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.gmail.com>
>> > Date: Tuesday, September 9, 2008 11:21 am
>> > Subject: Re: AMBER: D2O
>> > To: amber.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.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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Received on Thu Sep 11 2008 - 08:46:05 PDT
