[gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/1/17 4:28 PM, Alex wrote:
> Just a few quick questions for Justin.
> 
> I am looking at your tutorial, starting here:
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
> 
> 1. In your example, you have two pull groups. My understanding is that both
> are pulled relative to each other. In my case, the only thing that's pulled
> to create the series of configurations required for WHAM is a single ion,
> which is pulled relative to the rest of the system (nothing but a hydrated
> membrane with a particular type of hole inside of it). The ion starts above
> the hole, enters the hole, then leaves it, the aim here is to find the free
> energy associated with sitting in that hole.
> I recall (maybe incorrectly) that pull code has some quirks, so will your
> procedure work, or is there anything I should be aware of?
> 

Your situation is completely different.  Look into the cylinder settings for 
dealing with a layered system, but I have no experience with them.  To be clear 
- you always need two groups to define the vector (reaction coordinate) along 
which the bias is applied.  So you need to define a second group; you can't just 
say "I'm biasing an ion and that's it."

> 2. It is my understanding that only pullx and pullf files are required for
> WHAM, along with the tpr's for each of the MD runs, at least that's what
> follows from the tutorial. Anything about trajectories or energy files? May
> I just clean those up in my script, or will they be needed at any point?
> 

Might be useful for troubleshooting or inspecting the microscopic behavior that 
gives rise to the free energy profile.  There's always useful stuff there; 
rarely do you only care about just a single number coming out of WHAM.

-Justin

-- 
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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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