Re: namd-l digest V1 #2196

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Jun 09 2017 - 15:40:37 CDT

Dear Josh,

This is my first time using Umbrella Sampling and I was unable to catch all
of your information. I apologize for that. I am wondering how can I know my
umbrella will never move before finishing the analysis.
Thanks.

Rabeta Yeasmin

On Fri, Jun 9, 2017 at 1:07 AM, namd-l digest <
owner-namd-l-digest_at_ks.uiuc.edu> wrote:

>
> namd-l digest Friday, June 9 2017 Volume 01 : Number 2196
>
>
>
> In this issue:
>
> Re: namd-l: Umbrella Sampling colvar file parameters
> namd-l: Colvars wall boundaries for CoordNum
> Re: namd-l: Colvars wall boundaries for CoordNum
>
> ----------------------------------------------------------------------
>
> Date: Thu, 8 Jun 2017 17:32:44 +0000
> From: "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
> Subject: Re: namd-l: Umbrella Sampling colvar file parameters
>
> Hi Rabeta,
>
> They are not required to be set. Pay attention to the defaults in the
> documentation, since those are what is used if nothing is set. Width
> defaults to 1, which is just a scaling factor on the force constant you
> are using. 1 is usually fine, except when you are combining two
> different colvars into 1 reaction coordinate, and they are unequal. For
> umbrella sampling, boundary and wall constants are usually NOT set,
> since the harmonic section defines your umbrella. However, if you know
> your umbrella never moves, I suppose you could use upper and lower walls
> to define your potential instead of a single harmonic.
>
> - -Josh
>
> On 06/08/2017 11:26 AM, Rabeta Yeasmin wrote:
> > Hi,
> >
> > I am wondering if defining the width, boundary and wall constant in
> > the umbrella Sampling colvar file is a must. If so, how should I
> > define them means what parameters should I consider while defining
> > them. If these are not a must, Will using these parameters give any
> > extra benefit?
> >
> > Thanks.
> >
> > Rabeta Yeasmin
>
> ------------------------------
>
> Date: Fri, 9 Jun 2017 00:27:50 +0000
> From: Wasut Pornpatcharapong <wpornpat_at_mail.ucsd.edu>
> Subject: namd-l: Colvars wall boundaries for CoordNum
>
> Hi, I wonder if the actual force constant for CoordNumb s wall boundary is
> obtained from the b ForceConstantb in the colvars configuration file
> divided by the square of the width defined in colvars module for unbiasing
> usage?
>
> - -Wasut
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
> ------------------------------
>
> Date: Thu, 8 Jun 2017 20:42:46 -0400
> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Subject: Re: namd-l: Colvars wall boundaries for CoordNum
>
> Hi Wasut, the wall constant for a wall boundary is not rescaled (check the
> description of the physical unit):
> http://www.ks.uiuc.edu/Research/namd/2.12/ug/node55.html#SEC
> TION000132200000000000000
>
> The rescaling by width^2 is only needed because a harmonic bias can be
> defined on multiple variables, with very different units.
>
> Note, however, than in the latest versions you have the ability to define
> walls as a separate bias (and also change its force constant umbrella
> sampling-style). The current syntax that you are referring to will remain
> for backward compatibility.
>
> Giacomo
>
> On Thu, Jun 8, 2017 at 8:27 PM, Wasut Pornpatcharapong <
> wpornpat_at_mail.ucsd.edu> wrote:
>
> > Hi, I wonder if the actual force constant for CoordNumb s wall boundary
> is
> > obtained from the b ForceConstantb in the colvars configuration file
> divided
> > by the square of the width defined in colvars module for unbiasing usage?
> >
> >
> >
> > -Wasut
> >
> >
> >
> > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> > Windows 10
> >
> >
> >
>
>
>
> - --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
> ------------------------------
>
> End of namd-l digest V1 #2196
> *****************************
>
>

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