[gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/1/17 6:35 PM, Alex wrote:
>>
>>
>>>
>> You have a membrane with water on either side, yes?  That's a layered
>> system.
>>
>> But frankly, at this point I don't follow at all what you're trying to do.
>>
>> -
> 
> Let me try from the beginning. :)
> A membrane in XY, water on both sides. At the center of the membrane, there
> is a geometrically symmetric hole. A series of configurations exists,
> starting with the ion at +Z_0 above the membrane (along Z) and ending at
> -Z_0 below, only the Z coordinate is varying here. The center of the hole
> and the XY-position of the ion are very close, i.e. things are aligned (the
> series of configurations was generated in a pull simulation with the ion
> restrained in XY and pulled along Z). The goal is to find the free energy
> associated with ion's binding to the interior of the hole in membrane,
> nothing else. I can share the trajectory (without -sep), but only
> privately. Does this make sense?
> 
> Is there any reason you think I _cannot_ use your approach pretty much
> directly?
> 

Yes, because if your ion diffuses laterally (or whatever constitutes your 
"hole"), then you're not sampling what you think you're sampling.  That's what 
the cylinder geometry is for.  You have a system capable of significant lateral 
movement, so if you fail to apply a bias that acts in the x-y plane, your 
results are very quickly going to become garbage.

-Justin

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

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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