Re: [AMBER] concentration

From: Ilyas Yildirim <>
Date: Thu, 20 Jan 2011 13:26:24 -0600 (CST)

On Thu, 20 Jan 2011, Bill Ross wrote:

>> I am new in amber10. I want to simualte 1-6M urea with water . But I don't
>> know how make 1-6 M concentration of urea in amber 10.
>> How i make the system in different concentration?
> I think you will have to use trial and error, e.g. you could solvate
> a single urea with single urea's, then iteratively solvate that box
> with water until you get the right ratio. In pseudocode using leap:
> x = copy UREA
> solvatebox x UREA 5
> y = copy x
> solvatebox y TIP3BOX 15
> Knowing the total urea's in x, calculate the required number of
> waters, and keep making new y's and solvating with different radii
> until you get close enough to the desired result. Note that after
> a while, leap will eat up a lot of memory (the discarded cases),
> so it may be useful or necessary to stop leap and restart the process.
> Bill

Just to follow up what Bill said, if you are going to use constant
pressure dynamics, your initial box size will drop. So, my suggestion
would be to create a sample system as described by Bill, and then do a
regular minimization and pressure/temperature regulation. At the end,
pressure should be equilibrated and you can calculate the concentration of
urea. Then you can decide on how many urea you need to add or subtract
with respect to the number of waters in the system to bring it down to the
concentration you want.


AMBER mailing list
Received on Thu Jan 20 2011 - 12:00:02 PST
Custom Search