From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Nov 17 2020 - 03:50:14 CST
Hi Geordano,
Your Colvars Module configuration would look like this:
colvar {
name z
distanceZ {
main {
atomNumbers ... # The moving group
}
ref {
atomNumbers ... # The reference group
}
}
}
harmonic { # Define a moving harmonic restraint
colvars z
centers -10.0 # go from -10
targetCenters 10.0 # to 10 Angstrom
targetNumSteps 2000000 # in 2 million MD steps
forceConstant 10. # in kcal/mol/A^2
}
For an easier definition of the variable, eg. picking the correct atoms and checking that the values are what you expect, you can use the Colvars Dashboard in recent alpha versions of VMD.
In any publication using Colvars in NAMD, please don't forget to cite both the NAMD paper and the Colvars paper (https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594).
Best,
Jerome
----- On 16 Nov 20, at 23:16, Ropón-Palacios G. biodano.geo_at_gmail.com wrote:
> Dear NAMD users,
>
>
> I want run SMD simulation for generte windows to umbrella sampling, but
> like me making it using colvar module, is anybody can help me with an
> example, for favor.
>
> My sistem is an protein boudend to a ligand.
>
>
> Best for all,
>
>
> Geordano.
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