Re: we apply a harmonic potential

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun Jun 09 2019 - 15:18:55 CDT

Hello Jiali, the block that you used is sufficient to define a harmonic
restraint. If you run multiple independent simulations each with a
different restraint center, you are doing umbrella sampling. But it
requires that you set suitable initial conditions for each window.

targetCenters is used to change the restraint centers over time, and run
the windows sequentially. It is one (but not the only) way to set up
initial conditions for each window. You will probably also want
targetNumStages to define how many windows.

For details, see here:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic

On Sun, Jun 9, 2019 at 2:34 PM Jiali Wang <jwang204_at_binghamton.edu> wrote:

> Dear Giacomo,
> I am confusing when setting a umbrella sampling,in colvar file of harmonic
> part, I set as following:
> harmonic {
> name lenpot
> colvars length
> centers 5.0
> forceConstant 60.0
> }
> But I found tutorials mention need to set a target center,
> targetCenters 1.0
> targetNumSteps 2000000
> What I understand umbrella method is sampling ligand from center distance
> to target distance,by apply a harmonic potential, is that correct? If I
> don't set targetcenter, what's is this sampling means?
> Thank you for your help and your time!!
> best,
> Jiali
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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