From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Mar 16 2022 - 10:50:04 CDT
Thanks Giacomo for your comments. They were very helpful!
I will read through the document sections you pointed out.
Also, thanks for directing me to the python script. It will be useful...
Steve
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Wednesday, March 16, 2022 10:22 AM
To: NAMD list <namd-l_at_ks.uiuc.edu>; Seibold, Steve Allan <stevesei_at_ku.edu>
Subject: Re: namd-l: Colvar vs. SMD
Hi Steve, I was about to send this reply before seeing Jérôme's. The configuration is truncated, and I don't see in particular the part where the restraint center is moved. You should have "target*" options in the harmonic restraint config, as shown in this example:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_crash_course__;Iw!!DZ3fjg!v5heb0G2eJpIIciADl6ym5qPVwsbalDNIJv5z0ev2_DD6l_zctti_RWhpGD90g6zOA$ <https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fcolvars.github.io*2Fcolvars-refman-namd*2Fcolvars-refman-namd.html*23sec*3Acolvars_crash_course&data=04*7C01*7Cstevesei*40ku.edu*7Cb9a6f73841864b9e80c908da0760d0d5*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637830409671623669*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=57VF6a2E6*2FwZoJnBbceDFn5h8r7bRrdILbhk*2F*2FiSGeU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!v5heb0G2eJpIIciADl6ym5qPVwsbalDNIJv5z0ev2_DD6l_zctti_RWhpGDvSQPWvA$ >
You could also enable outputCenters and outputAccumulatedWork<https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fcolvars.github.io*2Fcolvars-refman-namd*2Fcolvars-refman-namd.html*23sec*3Acolvarbias_smd&data=04*7C01*7Cstevesei*40ku.edu*7Cb9a6f73841864b9e80c908da0760d0d5*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637830409671623669*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=Z*2Fm5AsuRv6zL8NSTNAcQClG8SHuskJ018X*2F9Q2B72rA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!v5heb0G2eJpIIciADl6ym5qPVwsbalDNIJv5z0ev2_DD6l_zctti_RWhpGBkvnKYdQ$ > to get a rough "PMF" (note the quotes: it's still SMD!), to process via your own plotting tools or this convenience script<https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fgithub.com*2FColvars*2Fcolvars*2Fblob*2Fmaster*2Fcolvartools*2Fplot_colvars_traj.py*3Fraw*3Dtrue&data=04*7C01*7Cstevesei*40ku.edu*7Cb9a6f73841864b9e80c908da0760d0d5*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637830409671623669*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=XV*2BBcSvVDcoizm18dpcnYZy5ujSTE93DtpgtAw6w52s*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!v5heb0G2eJpIIciADl6ym5qPVwsbalDNIJv5z0ev2_DD6l_zctti_RWhpGD9LuAPKQ$ >.
Specifically about Jérôme's question: there is an optional feature in Colvars' harmonic restraint that scales the force constant if width<https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=https*3A*2F*2Fcolvars.github.io*2Fcolvars-refman-namd*2Fcolvars-refman-namd.html*23sec*3Acolvar_grid_params&data=04*7C01*7Cstevesei*40ku.edu*7Cb9a6f73841864b9e80c908da0760d0d5*7C3c176536afe643f5b96636feabbe3c1a*7C0*7C0*7C637830409671623669*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=aA5*2Fgg*2FWe*2BMSqBys8H4Il4b9S2uTrkb9EnR7XkFWGDk*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!v5heb0G2eJpIIciADl6ym5qPVwsbalDNIJv5z0ev2_DD6l_zctti_RWhpGBwXqBuJw$ > is different from its default value of 1. This can be convenient if you choose forceConstant equal to kBT (~0.6 kcal/mol), in which case the width represents the standard deviation of the resulting distribution of the CV. For a simple distance or angle where you may have a good idea of the order of magnitude of the corresponding force constants, the default width = 1 can be more intuitive.
Just saw your latest message: indeed Jérôme was right and the source of the confusion was the scaling. But you should not have to pre-emptively worry about it unless you have a reason to change the default value of width. And if you do, the scaled force constant will always be printed to the output, which I highly recommend to check every time you are defining a restraint.
Giacomo
On Wed, Mar 16, 2022 at 9:23 AM Seibold, Steve Allan <stevesei_at_ku.edu<mailto: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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