[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Ok thanks Justin!
> On 28 Oct 2016, at 17:05, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 10/28/16 4:22 AM, gozde ergin wrote:
>> Thanks Justin,
>> 
>> Actually for my case I’ll put the methane molecule inside cubic box not spherical.
> 
> The geometry of the restraint is what is relevant.  If it's a spherical flat-bottom potential (the easiest thing to use) then you need to account for a spherical restriction.  The cube is periodic, so its shape is irrelevant.
> 
>> There is method called  'Boltzmann exponential reweighting’, however I could not figure out how to apply this method to methane-water system.
>> With the command of g_energy I could get the flat-bottom restraint energy, do you think I just need to remove these energy from the result \DeltaG?
>> I would like to learn if you have any idea and source to suggest.
> 
> It's not just something g_energy can subtract out; you're changing the entropy by a factor related to the volume.  It should be something like -RTln(V/V0) where V0 is the molar volume in the gas phase and V is the volume to which you are restricting the molecule.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 27 Oct 2016, at 20:58, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 10/27/16 11:35 AM, gozde ergin wrote:
>>>> Dear all,
>>>> 
>>>> I follow the Justin’s free energy calculations: Methane in Water tutorial. (Thanks Justin!)
>>>> I would like to ask two questions:
>>>> 
>>>> 1) Is there specific reason to use sd integrator?
>>> 
>>> Langevin dynamics gives better sampling.
>>> 
>>>> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>>>>   I would like to apply a flat-bottom restraint and keep methane molecule in the centre of bulk.
>>>>   I want to prevent methane movement in z direction.
>>>>   Do you have any idea how to remove the effect of flat-bottom restraint afterwards?
>>>> 
>>> 
>>> You're confining it to a spherical volume, so you need to account for that entropic contribution.
>>> 
>>> -Justin
>>> 
>>> --
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>>> Justin A. Lemkul, Ph.D.
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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 <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
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