From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 16 2022 - 09:41:02 CDT
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> 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>
> 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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