From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Mar 16 2022 - 10:18:38 CDT
Thanks for the responses! They have been helpful.
I did make an error by setting my width variable to 1 and scaling by 0.1. I was thinking that my width was set at 0.1; but, as you guys pointed out this is not the case. Oops. Something I should have noticed.
That’s where the #comment comes in.
Due to the scaling, I was thinking that 500 * 0.1^2 (width) =5 would mean I was really pulling with a force constant of 500. (Really high, I know. I was just doing it to pull off the peptide which seemed “stuck” to the surface.)
Steve
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Wednesday, March 16, 2022 9:41 AM
To: NAMD list <namd-l_at_ks.uiuc.edu>; Jérôme Hénin <jerome.henin_at_ibpc.fr>
Cc: Seibold, Steve Allan <stevesei_at_ku.edu>
Subject: Re: namd-l: Colvar vs. SMD
I wouldn't jump to conclusions, especially when the width parameter in the configuration is 1, not 0.1.
Steve, can you clarify for Jérôme and others what the comment represents? (Meanwhile I'll follow up with another reply to your original email.)
On Wed, Mar 16, 2022 at 10:30 AM Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>> wrote:
Hi Steve,
It seems you are scaling the intended force constant as if the width parameter were 0.1, but that is not the case in your current input. As it stands, the force constant is literally 5 kcal/mol/A^2.
Best,
Jerome
----- On Mar 16, 2022, at 2:21 PM, 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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