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
