Re: Multi-dimensional PMF

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Jul 27 2018 - 11:53:05 CDT

It could also mean finding if some of those degrees of freedom are more
important than others...

Jerome

On Fri, 27 Jul 2018 at 18:28, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Kelly,
>
> Figure out the appropriate 1-D pmf so that other collective variables are
> no longer corrupting. This might involve sampling a higher dimensional
> space, and then projecting down from that higher dimension to make a 1-D
> reaction coordinate. An example of this is the "pathCV" example provided in
> the colvars source (
> https://github.com/Colvars/colvars/blob/master/examples/10_pathCV.namd
> <https://github.com/Colvars/colvars/blob/master/examples/10_pathCV.namd).>),
> which basically defines a pathway based on distinct states, and
> interpolates between them. I've found the paper cited within to be very
> informative.
>
> -Josh
>
>
>
> On 2018-07-27 09:57:08-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Ah ok I see. In your experience, when other degrees of freedom in your
> system are corrupting your 1-D PMF, what is your process to deal with them?
> If it requires higher dimensions because you have to use more colvars, do
> you stay away from those situations? It was suggested to me that I bias the
> other orthogonal degrees of freedom, which is how I ended up at 5D.
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
> ------------------------------
> *From:* Jérôme Hénin <jerome.henin_at_ibpc.fr>
> *Sent:* Friday, July 27, 2018 9:16:44 AM
> *To:* McGuire, Kelly
> *Cc:* Namd Mailing List
> *Subject:* Re: namd-l: Multi-dimensional PMF
> What I meant between the lines is, don't do 5D PMFs.
> There are no ready-made tools to do the projection - if you get into this
> you'll have to be ready to write your own tools, and know the corresponding
> theory.
> Jerome
>
> On Fri, 27 Jul 2018 at 16:59, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> It's been a while since I've dealt with projections. Any suggestions on
> programs or the process you use to do that?
>
> Kelly L. McGuire
> PhD Scholar
> Biophysics
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602
>
> ------------------------------
> *From:* Jérôme Hénin <jerome.henin_at_ibpc.fr>
> *Sent:* Friday, July 27, 2018 1:45:20 AM
> *To:* Namd Mailing List; McGuire, Kelly
> *Subject:* Re: namd-l: Multi-dimensional PMF
> Hi Kelly,
> the only way to plot 5D data is to project it into lower-dimension spaces--0000000000000d563a0571fdf376--

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