[gmx-users] umberlla sampling

[Justin Lemkul]

On 3/18/16 5:21 AM, Ali Mohyeddin wrote:
> Dear Justin,
>
> In the tutorial of "umbrella sampling
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html>",
> what happens if we set the pull_coord1_rate to zero value? Does it work
> like a harmonic force (spring) between two groups with a constant distance
> averagely?  Indeed, I need to fix the distance between two groups and then
> start to pull them.
>

That's exactly what it does.

-Justin

> ;Pull code
> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = Chain_B
> pull_group2_name        = Chain_A
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = distance      ; simple distance increase
> pull_coord1_groups	= 1 2
> pull_coord1_dim         = N N Ypull_coord1_rate        = 0
> ; 0 nm per ps = 10 nm per ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_coor1_start        = yes           ; define initial COM distance >0
>
> Best regards,
>
> Ali Mohyeddin
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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