[gmx-users] Binning of Free Energy landscapes

[Justin Lemkul]

On 2/25/14, 8:30 AM, Ankita Naithani wrote:
> Hi Justin,
>
> Thank you for your reply. I actually wanted to know that for instance if my
> input to g_sham were my two principal components so would the bin indexes
> contain the frame numbers or time points? I get 1024 bins, and so I was
> confused as to how exactly and what does these indexes account for.
>

Offhand, I think the indexes refer to frame indices, but I haven't looked into 
that for a long time so I could be forgetting.  The source code will tell you 
for sure, or you can determine what's going on simply by what the numbers are - 
the distinction between the group sizes and values printed should be apparent.

-Justin

> Kind regards,
>
> Ankita
>
>
> On Tue, Feb 25, 2014 at 1:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/25/14, 4:54 AM, Ankita Naithani wrote:
>>
>>> Hi,
>>>
>>> I was wondering as to what exactly happens during the binning of Free
>>> Energy Landscapes as generated by g_sham? I generated Free Energy
>>> Landscapes using g_sham and my Principal Components but I am trying to
>>> understand what does bin account for and how exactly does it function?
>>>
>>>
>> It's just a histogram, with a bin width set using -bw.  The first
>> paragraph of g_sham -h describes what the calculations are.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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