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

From: Dickson, Callum <callum.dickson.novartis.com>
Date: Tue, 17 Jul 2018 14:47:22 +0000

-----Original Message-----
From: zmatovic.kg.ac.rs [mailto:zmatovic.kg.ac.rs]
Sent: Monday, July 16, 2018 5:33 AM
To: amber.ambermd.org
Subject: [AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule?
Importance: High

 

Dear Callum and othe AMBER people,

I red very carefully, Callum tutorial
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_callumjd_AMBER-2DUmbrella-5FCOM-5Frestraint-5Ftutorial&d=DwIFBA&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=2vM6z3xs1toKPZ95oRtJ883OvQ6DlwhsXwqKsJv0fBg&s=280BRdGBD31G76e4E2Kz9J_xNOoBEek6BCq6T3r0AZE&e= 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?

This is the number of bins you use in WHAM - this number is still fine but you can vary it and see the effect.


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?

You run the ACF for each of the 32 windows, so just update the settings accordingly.


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)?

To compute the partitioning you integrate the free energy curve but I've seen different ways to normalize the result and connect with experiment - I'd consult the literature on this.


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. MatoviŠ, professor of chemistry

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Received on Tue Jul 17 2018 - 08:00:04 PDT
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