[gmx-users] questions about umbrella sampling

[Justin Lemkul]

On 3/4/15 9:47 AM, 凌未风 wrote:
> Hello everyone:
>
> I am trying to do PMF calculation by umbrella sampling, and I would like to control the distance between two lipid molecules on the plane of membrane bilayer (i.e., the x-y plane). I have a question of how to implement it in gromacs, because in gromacs, if we are doing umbrella sampling, we have to use the pulling code as follows:
>
> pull            = umbrella
> pull-geometry   = distance  ; simple distance increase
> pull-dim        = Y Y N
> pull-vec1       = 0 0 0
> pull-start      = yes       ; define initial COM distance > 0
> pull-ngroups    = 1
> pull-group0     = group0
> pull-group1     = group1
> pull-rate1      = 0.001         ; pull rate, 6nm finished in 60ns
> pull-nstxout    = 500
> pull-nstfout    = 500
> pull-k1         = 4500      ; kJ mol^-1 nm^-2 ; try smaller one,
>
> when we try to pull the two groups away, we have to define the direction of the pulling force.
> My question is: how to define "pull-dim" and "pull-vec1" if I would like to control the distance between the center of mass of two lipid molecules on the membrane plane. In my case I have to control the distance on the x-y plane, which is sqrt(x^2+y^2). How could we do this in gromacs?

You don't need both.  The distance geometry uses pull-dim, not pull-vec1.

> If we would like to control the distance in on direction, e.g., the distance along the z direction, it is straightforward, we could define pull-dim= N N Y, and pull-vec1=0 0 1. But in my case how could we do it? Or we have to use plumed package to implement it?
>

pull-dim = Y Y N should accomplish what you need.

-Justin

> Thanks for your help. Look forwarding to hearing from someone.
>
> With my best regards,
> RXG
>

-- 
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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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