Re: Multi-dimensional PMF

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Jul 27 2018 - 13:07:51 CDT

Thanks Josh, just to be clear when you say project down from 5D to 1D you do mean a vector projection from the 5D output values to a 1D vector?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Friday, July 27, 2018 10:27:45 AM
To: McGuire, Kelly; jerome.henin_at_ibpc.fr
Cc: namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Multi-dimensional PMF

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).>), 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<mailto: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<mailto: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. A 5D space is also difficult to sample. Typically we'll try to make our colvar space as low-dimension as possible, to make our life simpler.
Jerome

On Thu, 26 Jul 2018 at 23:43, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

So, everything seems to be working having a distanceZ colvar and 4 dihedral colvars (to bias the 4 histidine sidechains in my ion channel). But, now that means I have a 5-D .grad and .count, instead of just the 1-D .grad and .count which writes a 1-D PMF. I know how to use abf_integrate and got that to work to create a PMF. But, we are wondering how to even begin plotting data beyond 1, 2, and 3-D...

The reason I am biasing those four dihedrals is because our 1-D PMF was skewed, meaning bulk water on the c-terminus side of the ion channel is 30-50 kcal/mol higher than bulk water on the n-terminus side (they should be the same energy). We believe this energy value corruption is due to these histidines, so we are biasing them. We would like to see if this fixed the corrupted energy values on the 1-D PMF, how would we go about doing that?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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