[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thanks Justin,

Actually for my case I’ll put the methane molecule inside cubic box not spherical. 
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.
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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