[gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

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
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================