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

From: Daniel Scott <dscott5.nd.edu>
Date: Thu, 16 Dec 2010 15:05:56 -0500

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
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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Received on Thu Dec 16 2010 - 12:30:01 PST
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