Re: [AMBER] unit conversion during umbrella sampling and then PMF calculation

From: Song, Lin <>
Date: Wed, 18 Sep 2019 16:27:28 +0000

Hi Satyajit,

I wanna share my suggestions for WHAM and if it’s not correct, anyone in the mailing list can correct me.

First the unit for WHAM should be kcal/(mol*A^2). Second, the tolerance value I’d use is 0.0001.


> On Sep 18, 2019, at 4:06 AM, SATYAJIT KHATUA <> wrote:
> Dear AMBER users,
> Recently, I have done umbrella sampling for
> PMF calculation using PLUMED plugin coupled with AMBER for a ligand-bound
> protein. The conventional unit of spring constant is [energy units of the
> program] / [units of the CV]^2. So after completing my umbrella sampling
> with let's say 34 bins, we go for WHAM to generate PMF. For PLUMED, units
> of the spring constant are kJ/mol/[nm]^2. Now for the calculation in WHAM,
> I have to transfer units to kcal/mol/[nm]^2. For my case, I have taken the
> spring constant of 300 kJ/mol/nm^2 and after conversion, the value is like
> 71.702 kcal/mol/nm^2. Although the WHAM program uses 0.5k(x-x0)^2, so we
> have to multiply the original force constant by 2. So, the final value of
> the spring constant is 143.404 kcal/mol/nm^2. After running WHAM, I am
> getting the PMF values which are continuously increasing. So, am I doing
> anything wrong with the unit conversion step? or there is something wrong
> about tolerance value from my side (taken as 0.01) in WHAM?? Please help me
> out.
> thanks in advance,
> Satyajit Khatua,
> Dept. of Chemistry,
> IIT Kharagpur,
> Kharagpur-721302.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Sep 18 2019 - 09:30:01 PDT
Custom Search