[gmx-users] Pull code vs. manual pull for umbrella sampling

Justin Lemkul jalemkul at vt.edu
Mon Jan 27 22:00:19 CET 2014

On 1/27/14, 3:49 PM, shivangi nangia wrote:
> Hello,
> As I had explained earlier, I have done MD at varied protein bi-layer distances.
> I now want to create a probability distribution histogram along the reaction
> coordinate I generated by varying the distances.
> I know I can concatenate various .trr files I have from various MD runs with
> different initial starting configurations.

There is no need to concatenate trajectories.  In fact, that will probably make 
your life harder having one massive trajectory.  I suspect you'll want the 
distributions from each individual trajectory, anyway.

> Is there a way to obtain the probability distribution histogram.

That's what g_analyze -distr does.  Feed it the output of g_dist.



Justin A. Lemkul, Ph.D.
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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