[gmx-users] Re: g_wham

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Thanks Justin
> 
> Is it possible to use g_wham with pull_geometry = direction, I read on
> the website that you couldn't but was wondering if this had changed?
> 

Nothing has changed as far as I am aware.  Also keep in mind the difference 
between SMD and umbrella sampling.  They are separate procedures, as hopefully 
my tutorial has made clear.

-Justin

> Gavin
> 
> Justin A. Lemkul wrote:
>>
>> Gavin Melaugh wrote:
>>> Hi All
>>>
>>> I am using COM pulling to pull two molecules together in order to
>>> calculate the potential of mean force and the pulling is fine. I am
>>> using pull = umbrella for the pulling as I am following
>>>  the tutorial on the website. If I use pull = constraint does this still
>>> pull the molecules together, and if so do you still then need to
>>> perform umbrella sampling on the configurations generated? I am a little
>>> confused  as I don't understand how the molecules pull together if they
>>> are constrained.
>>>
>> For plain SMD, you can use any of the pull methods.  In the tutorial I
>> wrote, I explain why I used "pull = umbrella" during SMD.  Umbrella
>> sampling is a separate procedure, which can be done after SMD.  If you
>> want a free energy along the reaction coordinate, there are several
>> methods for doing this, among which is umbrella sampling.
>>
>> -Justin
>>
>>> Many Thanks
>>>
>>> Gavin
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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