Re: [AMBER] Issues with Calculating P^2 values with RMS fits

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 17 Dec 2010 00:32:02 -0500

Hello,

My comments are below:

On Thu, Dec 16, 2010 at 3:05 PM, Daniel Scott <dscott5.nd.edu> wrote:

> Dear Amber community,
> I have run 20 ns MD simulations on a small molecule
> (Fluorescein-5-maleimide) and am trying to calculate the S^2/P^2. Below
> are
> the two different ptraj commands I have used, one defining the rms fit
> using
> an average-coordinate pdb, the other using the first command. After
> plotting the results I get different P^2 functions. How are these different
> RMS flags affecting the P^2? And which one is best for calculating S^2
> (the
> asymptote of P^2) and rotational constants?
>
> Thanks for any advice,
> Dan Scott
>
> ----------THE AVERAGE REFERENCE CALCULATION---------------------
>
> trajin F5M_0_md_prod_1.mdcrd.gz.........
> trajin F5M_0_md_prod_20.mdcrd.gz
>
> strip :WAT
>
> average F5Mavg.pdb pdb
>

Careful here! average F5Mavg.pdb pdb is not doing what you think it's doing
(I believe). This average structure will look all kinds of wacky (visualize
it to see). The problem is that average simply averages the values of the
cartesian coordinates over the whole trajectory, which incorporates various
translational and rotational motions which will get added into the average.
I don't think this is what you want. You should run a separate ptraj script
to first create the average:

trajin trajectory......
trajin trajectory2.....

strip :WAT

rms first [mass]
average F5Mavg.pdb

Then run the above script. That will create the average PDB (this one should
look better!). You may find that using "first" and reference to the average
may be far more similar now. However, I'm not familiar enough with
time-correlation functions to give you a definitive answer on that.

Hope that helps,
Jason

reference F5Mavg.pdb
> rms reference out F5Mavg.rms name F5Mavgcorrrms
> vector O2C9 .2 corr @9
> vector C11C12 .11 corr @12
> analyze timecorr vec1 O2C9 tstep 200 tcorr 20000000.0 out
> O2C9tstep200corrrmsavg.out
> analyze timecorr vec1 C11C12 tstep 200 tcorr 20000000.0 out
> C11C12tstep200corrrmsavg.out
>
> -----------VERSUS THE RMS FIRST CALCULATION-------------------------------
>
> strip :WAT
> rms first out F5Mfirst.rms
> vector O2C9 .2 corr @9
> vector C11C12 .11 corr @12
> analyze timecorr vec1 O2C9 tstep 200 tcorr 20000000.0 out
> O2C9tstep200corrrmsfirst.out
> analyze timecorr vec1 C11C12 tstep 200 tcorr 20000000.0 out
> C11C12tstep200corrrmsfirst.out
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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Dec 16 2010 - 22:00:02 PST
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