[gmx-users] Binning of Free Energy landscapes
ankitanaithani at gmail.com
Tue Feb 25 14:30:25 CET 2014
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.
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:
>> 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 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
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