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

From: <zmatovic.kg.ac.rs>
Date: Tue, 17 Jul 2018 18:03:11 +0200

Thanks Callum,
I calculated PMF and the line appears to be of better quality.

However, when try to run : "./ACF_calc.x -f ./dist_32.0/prod_dist.dat -s
300000 -n 300000 -d 0.02 -o acf_plot.dat" it goes in infinity.
Once again it's a 1Ang. separated windows followed by production run each
30 ns. Is above run OK or I should change something?

Thank You helping me.

Regards,
Zoran

-----Original Message-----
From: Dickson, Callum <callum.dickson.novartis.com>
Sent: Tuesday, July 17, 2018 4:47 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Determination of pmf, diffuse, permeability and
resistance in case of lipid molecule?



-----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_AMB
ER-2DUmbrella-5FCOM-5Frestraint-5Ftutorial&d=DwIFBA&c=ZbgFmJjg4pdtrnL2HUJUDw
&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=2vM6z3xs1toKPZ95oRtJ883OvQ6
DlwhsXwqKsJv0fBg&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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailma
n_listinfo_amber&d=DwIFBA&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430r
dz1DD2LkJxNM3BsKSjrw&m=2vM6z3xs1toKPZ95oRtJ883OvQ6DlwhsXwqKsJv0fBg&s=Vqcx4GE
Kq5ChZa9fDLXU1-50oHjHH5wCIStutEfXYXk&e=

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 17 2018 - 09:30:03 PDT
Custom Search