[AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule?

From: <zmatovic.kg.ac.rs>
Date: Mon, 16 Jul 2018 11:33:26 +0200


Dear Callum and othe AMBER people,

I red very carefully, Callum tutorial
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial and took
the windows separated by 2 A, with each window being run to 5 ns and the
z-position being written every 10th step (istep=10) (manual). Hovewer, PMF
curve didn't look so nice. So, I decided to extend umbrella-windows method
by 1 A spacing, 30 ns run time and istep=1.


My questions are:

1. For running wham of latter after dynamics, is the number of windows
(320) in the script "wham 0 32 320 0.00000001 303 0 metadata.dat out.pmf"
variable or correct in case of 30ns?
2. Autocorrelation function in my case should be: "./ACF_calc.x -f
../dist_32.0/prod_dist.dat -s 300000 -n 300000 -d 0.02 -o acf_plot.dat"
3. I hope after these suggestions I'll be able to calculate all the
parameters (using given Callum tutorial). However I wonder how can I
calculate partition coefficient using all calculated data. Is there any
script (excel help)?


I would appreciate your help very much.


Best regards,


A true friend is someone who is there for you

when he'd rather be anywhere else.

-- Len Wein


Dr Zoran D. MatoviŠ, professor of chemistry

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Received on Mon Jul 16 2018 - 03:00:02 PDT
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