Re: Colvar vs. SMD

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon Mar 21 2022 - 09:21:39 CDT

Dear Steve,

Hello, fellow Kansan. It sounds like you are trying to calculate the
adsorption affinity of a relatively small molecule for an interface
(my apologies if I'm wrong). SMD is usually not the best choice for
this. I typically use ABF (or if sampling in ABF is difficult,
replica-exchange umbrella sampling). This is something I do pretty
routinely, as you can see from these papers:

https://urldefense.com/v3/__https://doi.org/10.1021/acsnano.5b03592__;!!DZ3fjg!puCi-9VvNetdKAR80yMn_poFEi7KoUIJ3z908POn0jsjmf2e6IGy45jmc6CKVkddcw$
https://urldefense.com/v3/__https://doi.org/10.1021/acs.jctc.8b00830__;!!DZ3fjg!puCi-9VvNetdKAR80yMn_poFEi7KoUIJ3z908POn0jsjmf2e6IGy45jmc6Dc2NnLNQ$
https://urldefense.com/v3/__https://doi.org/10.1039/D1NA00570G__;!!DZ3fjg!puCi-9VvNetdKAR80yMn_poFEi7KoUIJ3z908POn0jsjmf2e6IGy45jmc6DGGaq6Zw$

Colvars will give you a .pmf file that represents the free energy as a
function of distance from the interface:

colvar {
  name SurfZ

  width 0.05
  lowerBoundary 3.2
  upperBoundary 25.0
  outputValue on
  outputAppliedForce on

  distanceZ {
    # Adsorbate molecule
    main { atomNumbersRange 1-47 }
    # Atoms of upper surface layer
    ref { atomNumbersRange 48-383}
  }
}

abf {
  colvars SurfZ
  fullSamples 200
  historyFreq 250000
}

harmonicWalls {
  colvars SurfZ
  lowerWalls 3.2
  upperWalls 25.0
  forceConstant 10.0
}

If you're interested in trying this, my group has a tutorial that
might be helpful as well.

https://urldefense.com/v3/__http://jeffcomer.us/tutorials.html__;!!DZ3fjg!puCi-9VvNetdKAR80yMn_poFEi7KoUIJ3z908POn0jsjmf2e6IGy45jmc6Cza-Uifg$

Regards,
Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: 334 Coles Hall
Phone: 785-532-6311
Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!puCi-9VvNetdKAR80yMn_poFEi7KoUIJ3z908POn0jsjmf2e6IGy45jmc6DGDPCZKQ$

On Wed, Mar 16, 2022 at 8:23 AM Seibold, Steve Allan <stevesei_at_ku.edu> wrote:
>
> Hello
>
> I am pulling a peptide from metallic surface using NAMD. I am comparing the process using SMD and Colvars. I have found that I have to use a substantially higher (over 10 times) force constant with Colvars than I do using SMD to remove the peptide from the surface.
>
> My concern is that I am doing something incorrect in setting up my Colvars script shown below. I would appreciate any insights..
>
> Thanks, Steve
>
>
>
> colvar {
>
> name Translocation
>
>
>
> width 1.0
>
>
>
> lowerboundary 7.50
>
> upperboundary 17.512
>
>
>
> lowerwallconstant 100.0
>
> upperwallconstant 100.0
>
>
>
> outputvelocity on
>
>
>
> distanceZ {
>
> main {
>
> atomnumbersrange { 1-90 }
>
> }
>
> ref {
>
> atomnumbers { 902
>
>
>
> }
>
> }
>
> axis ( 0.0, 1.0, 0.0 )
>
> }
>
> }
>
>
>
> harmonic {
>
> name Y
>
> colvars Translocation
>
> centers 13.0
>
> forceConstant 5.0; # 500 * 0.1^2 = 0.1
>
>

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