[gmx-users] Binning of Free Energy landscapes

[Ankita Naithani]

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.

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Ankita Naithani