Re: Multi-dimensional PMF

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Jul 28 2018 - 09:48:08 CDT

Neither amantadine nor your new complexes permeate the channel, so asking how large the barrier would be if they were shot through it like a bullet (what you’re effectively doing given the time scales) doesn’t seem particularly relevant. Presumably a better question is how tightly they bind and in what position/orientation. The former would require complicated free-energy calculations (absolute binding free energy) that are very difficult to converge. The latter may require nothing more than very long (~1-10 μs) equilibrium simulations.

I’ve found a tendency (even for myself) to fall back on free-energy calculations as a shortcut to thinking carefully about the problem/system at hand. For example, instead of trying to calculate a complex multi-dimensional PMF for folding of a protein, we’re turning to steered MD to look at unfolding, which is sufficient to discriminate between our hypotheses. A lot of times you don’t actually need a precise number and even more of the time, you probably can’t reliably get it anyway.

Best,
JC

> On Jul 28, 2018, at 12:25 AM, McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> Thanks for all the responses. I should shed so more light on our current project. The ligand that is being used currently in these ABF simulations is amantadine. Its PMF will serve as a control for other ABF simulations. We have designed and tested novel copper-complexes that block this channel (both wild-type and the S31N mutant). They are believed to bind the imidazoles on the histidines. Now, I am headed toward running ABF simulations with these complexes. It seems my P.I. wants a PMF of the full channel in order to get the free energy near the histidine/trytophan complex (to have this to compare with the PMF of our new copper-complexes) and to do a sanity check of the free energy beyond that complex into bulk water, which should match the free energy of the bulk water near the entrance of the channel.
>
> Now, I recognize that CHARMM does not have very good parameters for Cu(II), so eventually I'll need to do a QM/MM ABF. I am also using GAUSSIAN09 to do some coordination studies at the histidine complex. We just wanted to start with a lower theory (MM ABF) and work our way up one step at a time, doing checks along the way.
>
> We know amantadine can't get through the his/trp complex, the barrier is going to be too large, but we are wondering how large. But, perhaps there is too much corruption in the energy because the barrier is so large and there are a lot of variables that come into play.
>
> Maybe our approach should be to only do ABF up to the histidines and not beyond...? Maybe there is a better free energy method to use than ABF for our particular problem...
>
>
> Kelly L. McGuire
> PhD Scholar
> Biophysics
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602
>
> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Sent: Friday, July 27, 2018 9:49:55 PM
> To: NAMD list; Jeff Comer
> Cc: McGuire, Kelly
> Subject: Re: namd-l: Multi-dimensional PMF
>
> Hello, all.
>
> Not to curb everyone's enthusiasm, but this particular channel has three constriction regions. The innermost one, which is being discussed, is composed by four histidines. The second innermost one has four tryptophans packed together even more tightly. Depending on the viral strain there can be also a tetrad of valines at the outer opening, aptly called a "valve" by the crystallographers who resolved it.
>
> At four additional variables for every region, that could really get out of hand.
>
> Kelly, while it would be very effective to use collective variables-based simulations to compute a PMF, have you thought about initializing the ligand in multiple positions and run regular MD simulations on each one? If done carefully, this could actually carry some information about the permeation process, and use more of the computer's time than yours (always a good thing for a computational scientist).
>
> Giacomo
>
>
>
> On Fri, Jul 27, 2018 at 7:41 PM Jeff Comer <jeffcomer_at_gmail.com <mailto:jeffcomer_at_gmail.com>> wrote:
> Dear Kelly,
>
> If you are interested in the free energy along all five dimensions, you can
> usually do 1D ABF (which often helps with sampling along all degrees of
> freedom) and reweight to obtain PMFs along other directions. In this paper
> ( http://doi.org/10.1021/acs.jcim.7b00521 <http://doi.org/10.1021/acs.jcim.7b00521> ), we generate a 3D PMF from a
> trajectory where ABF was applied along a single dimension. See equation 1.
> To do this, you should store a lot of frames or use Colvars to get good
> statistics on your other dimensions.
>
> In any case, I do 2D and 3D ABF pretty regularly. In this paper (
> http://doi.org/10.1021/acs.jpcb.7b01130 <http://doi.org/10.1021/acs.jpcb.7b01130> ), we use a volumetric
> representation for the 3D PMF (see Figure 3A), although it's not that easy
> to look at. You can either integrate these PMFs into lower dimensions or
> take slices out of them. Slices aligned with the collective variable axes
> can be done easily with awk, Matlab, etc. We made 2D heat maps using slices
> of the 3D PMF (see Figure 3B,C,D). You can also integrate 2D and 3D PMFs to
> obtain lower dimensional PMFs (Figure 3F). If the inclusion of the extra
> dimensions is to get better sampling along the primary dimension, then all
> you really care about is this 1D PMF anyway. In the limit where sampling is
> good along the other dimensions in the absence of multidimensional ABF, 1D
> ABF and 3D ABF integrated down to one dimension give the same results.
>
> One warning: 3D ABF requires a lot of sampling and larger "widths" than
> you'd use for 1D ABF (to avoid having millions of bins). 4D might be
> possible...
>
> Have fun,
> Jeff
>
>
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us <http://jeffcomer.us/>
>
> On Fri, Jul 27, 2018 at 2:43 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov>>
> wrote:
>
> > No, I mean figure out what parts of the variables are actually relevant to
> > the transition you are trying to describe and make it 1-D. The pathCV is
> > just useful if you can't entirely get a handle on what *specifically* is
> > changing, but you know that something is, since RMSD to a target hides a
> > multitude of sins. Multidimensional sampling, while technically doable,
> > is expensive to do properly, since the amount of sampling required for
> > convergence is polynomial in the number of dimensions. So 1D is ideal, 2D
> > is doable, and anything beyond is unheard of.
> >
> > If it were me, I'd use a regular distanceZ on the parts away from the
> > histidines, and just focus sampling on the transition like crazy. This
> > sounds like a selectivity filter for the channel, where the ions tend to
> > dehydrate quite substantially, and you get a hard-to-sample region of your
> > PMF. How long did you run your 1D stuff again? Di Maio et a.
> > (10.1371/journal.pone.0140258) ran for 20ns a window, and while their
> > sodium PMF closes (equal free energies in solution), their chloride PMF
> > does not, and seems to "remember" being dragged across the membrane to
> > start the simulation.
> >
> > -Josh
> >
> >
> >
> > On 2018-07-27 12:07:57-06:00 McGuire, Kelly wrote:
> >
> > 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 <mailto:Joshua.Vermaas_at_nrel.gov>>
> > *Sent:* Friday, July 27, 2018 10:27:45 AM
> > *To:* McGuire, Kelly; jerome.henin_at_ibpc.fr <mailto:jerome.henin_at_ibpc.fr>
> > *Cc:* namd-l_at_ks.uiuc.edu <mailto: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/ <https://github.com/Colvars/>
> > colvars/blob/master/examples/10_pathCV.namd
> > <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FColvars%2Fcolvars%2Fblob%2Fmaster%2Fexamples%2F10_pathCV.namd).&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C93b1b9fdafa5441aafc208d5f3ebdfd2%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636683116767237649&sdata=fK6fJBRd%2F1iVSVhTkYjHVQLS0KYWOAW0qaei8S0cVNo%3D&reserved=0 <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FColvars%2Fcolvars%2Fblob%2Fmaster%2Fexamples%2F10_pathCV.namd).&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C93b1b9fdafa5441aafc208d5f3ebdfd2%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636683116767237649&sdata=fK6fJBRd%2F1iVSVhTkYjHVQLS0KYWOAW0qaei8S0cVNo%3D&reserved=0>>),
> > 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 <mailto: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 <mailto: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
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>

This archive was generated by hypermail 2.1.6 : Mon Nov 18 2019 - 23:20:01 CST