Hi Sid,
I think your second procedure is the correct one.
You vary r2,r3 with the values of this distance you are interested in.
Typically r1 < r2 = r3 < r4. r2 and r3 should be close to the value you want
the distance to be in a particular window while r1 and r4 should be far away
if you want a harmonic potential (page 103 amber 11 manual). You need a
different restraint file for each window.
You will have to choose the range for the distance based on what makes sense
for what you are doing.
Emmanuel.
On Mon, Apr 4, 2011 at 9:50 AM, siddesh southekal
<siddeshonline.gmail.com>wrote:
> Umbrella sampling
>
> Dear all,
>
> I am new to umbrella sampling and i am bit confused about the procedure
> and
> i would be glad if you can clear my doubts.
> I want to use umbrella sampling to checkthe free energy profile during
> conformational change of protein along a particular reaction coordinate .
> (for example distance between two atoms )
>
> As i understand we run a series smaller simulations such that the restart
> file (.rst) generated at the end of one simulation (window1 ) is used as
> input (starting structure) for the next simulation ( window 2) and then the
> result is used for WHAM analysis. Naturally this becomes very tedious ;) .
>
> or do we run independent simulations (using different restraint file-
> varying the values of r1, r2, r3, and r4 ) using same starting structure
> (.crd file) as described in Dr.Tings tutorial ? (
> http://projects.eml.org/mcm/people/wang/PMF/tutorial.html) .But then i
> need
> to have different restraint files.If i want to hthe distance to be around
> 14A can i start with r2=r3=0 (on what basis do we vary the values of r2
> and
> r3 - is there a particular range ) .
>
> # distance restraint
> &rst iat=1402,4276, r1=-100.0, r2=14.0, r3=14.0, r4=100.0, rk2 = 30.0,
> rk3
> = 30.0, /
>
> how do i do it ?
>
> Thanks for the suggestion
>
> sid
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Received on Mon Apr 04 2011 - 09:30:07 PDT
