RE: Colvar vs. SMD

From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Tue Mar 22 2022 - 08:17:33 CDT

Dear Jeff
Thanks so much for the links to your papers and for your suggestions. I am reading through your papers now. Yes, I am attempting to understand the nature of small peptides' binding to and recognition of surfaces.
I will enjoy going through your tutorial using ABF and attempt to utilize ABF with my present system...

Cheers, Steve

-----Original Message-----
From: Jeff Comer <jeffcomer_at_gmail.com>
Sent: Monday, March 21, 2022 9:22 AM
To: Seibold, Steve Allan <stevesei_at_ku.edu>; NAMD list <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Colvar vs. SMD

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://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fdoi.org*2F10.1021*2Facsnano.5b03592&amp;data=04*7C01*7Cstevesei*40ku.edu*7Ce39dba2bf9364feabb3108da0b46306b*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637834693816433898*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&amp;sdata=GmUrOp4fYQrXOSeSpGghUKgy*2B9PwdwaTHHbJG0T1kF4*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!pFZ_fU9Iq0Wv7-5YySSJFcJpRhr0LvEvVKmv4QA3pvthH_68URwYOQl-Er0KBmBBoA$
https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fdoi.org*2F10.1021*2Facs.jctc.8b00830&amp;data=04*7C01*7Cstevesei*40ku.edu*7Ce39dba2bf9364feabb3108da0b46306b*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637834693816433898*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&amp;sdata=*2BD2wmwVJogOv4CjxHx*2FNPAEP6qiO9huvXQm5GqVTShA*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!pFZ_fU9Iq0Wv7-5YySSJFcJpRhr0LvEvVKmv4QA3pvthH_68URwYOQl-Er35NbpyVA$
https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fdoi.org*2F10.1039*2FD1NA00570G&amp;data=04*7C01*7Cstevesei*40ku.edu*7Ce39dba2bf9364feabb3108da0b46306b*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637834693816433898*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&amp;sdata=AScv*2FMKdAGAGu0Yczw47G6DK9n3rsShV*2BRU1HYH8lpQ*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!pFZ_fU9Iq0Wv7-5YySSJFcJpRhr0LvEvVKmv4QA3pvthH_68URwYOQl-Er0InX2ODA$

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/__https://nam10.safelinks.protection.outlook.com/?url=http*3A*2F*2Fjeffcomer.us*2Ftutorials.html&amp;data=04*7C01*7Cstevesei*40ku.edu*7Ce39dba2bf9364feabb3108da0b46306b*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637834693816433898*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&amp;sdata=4pR4bkD4lZJCjXgK54gqnAeToUXRJSYC*2FKo*2FNziBiA8*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!pFZ_fU9Iq0Wv7-5YySSJFcJpRhr0LvEvVKmv4QA3pvthH_68URwYOQl-Er1-Q3HtPQ$

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/__https://nam10.safelinks.protection.outlook.com/?url=http*3A*2F*2Fjeffcomer.us*2F&amp;data=04*7C01*7Cstevesei*40ku.edu*7Ce39dba2bf9364feabb3108da0b46306b*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637834693816433898*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&amp;sdata=h3WjJAFBX*2BzTQ9xoKCEdr3NyYrZfljSwhHfe6onqa8M*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!pFZ_fU9Iq0Wv7-5YySSJFcJpRhr0LvEvVKmv4QA3pvthH_68URwYOQl-Er1_RQTXPw$

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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