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"
true?
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,
Zoran
A true friend is someone who is there for you
when he'd rather be anywhere else.
-- Len Wein
Dr Zoran D. Matoviæ, professor of chemistry
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 16 2018 - 03:00:02 PDT
