AMBER Archive (2008)

Subject: RE: AMBER: tip3p water and shake

From: Wang,Ying (wangying_at_ufl.edu)
Date: Wed Jun 18 2008 - 20:03:55 CDT

Thanks a lot!

I will try it.

Best,

Ying

On Wed Jun 18 17:35:30 EDT 2008, Ross Walker
<ross_at_rosswalker.co.uk> wrote:

> Hi Ying,
>
> The TIP3P water model was parameterized specifically for use with
> shake,
> hence turning off shake for TIP3P will result in the water model
> no longer
> providing satisfactory results.
>
> If you really want to run your solute without shake then you can
> use the
> shakemask variable to only shake the water atoms (you still need
> a time step
> of 1fs or less though). Alternatively you could use a flexible
> water model
> like spcfw.
>
> Good luck,
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
>> On Behalf
>> Of Wang,Ying
>> Sent: Wednesday, June 18, 2008 1:07 PM
>> To: amber_at_scripps.edu
>> Subject: AMBER: tip3p water and shake
>>
>> Dear all,
>> If I perform a simulation in explicit solution, like tip3p
>> waterbox, could I turn off shake? because manual say that tip3p
>> water like a rigid triangle but if turn off shake the bond length
>> involve hydrogen will be changed. So I'm worried about that and
>> ask you. Thank you very much!
>>
>> Best,
>>
>> Ying
>>
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> 

--
Wang,Ying

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