[gmx-users] constant velocity pulling/Umbrella sampling

[Justin Lemkul]

On 3/12/13 7:45 AM, raghav singh wrote:
> Hello Fellow Users,
>
> I have a doubt about the mdp option in case of constant velocity pulling /
> Umbrella pulling simulation.
>
> pull            = umbrella
> pull_geometry   = distance      ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A**pull_rate1      = 0.01          ; 0.01 nm
> per ps = 10 nm per ns
> **pull_k1         = 1000          ; kJ mol^-1 nm^-2*
>
> Pull_rate1 = velocity variable for CVP
> Pull_k1    = is this option is for constant force pulling OR THIS IS SPRING
> CONSTANT FOR THE VIRTUAL SPRING???
>
> because i am trying to follow Justin's umbrella sampling tutorial and when
> i remove this PULL_K1 option...then the COM Pull Energy ... does not change
> and the ligand never get pulled away.??
>

Per the manual:

"The force constant. For umbrella pulling this is the harmonic force constant in 
[kJ mol-1 nm-2]. For constant force pulling this is the force constant of the 
linear potential, and thus minus (!) the constant force in [kJ mol-1 nm-1]."

If you do not specify it in the .mdp file, its default value (again, in the 
manual) is zero, so it will of course do nothing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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