[gmx-users] Pull code vs. manual pull for umbrella sampling
shivangi.nangia at gmail.com
Tue Jan 28 02:13:39 CET 2014
Thanks for the reply.
I have a follow up question.
I used g_dist to obtain the COM distance between the protein and bi-layer
at one particular starting configuration.
As you suggested, I fed the dist.xvg file into g_analyze.
However, the output from g_analyze i.e. distr.xvg file contains "&" symbols.
I know g_analyze "reads" in files with "&" in them and can process it.
What does "&" tell in an output file by g_analyze?
Is it the distribution in sets? first data set of distribution for time say
200 ps then separated by & another distribution data set for 400 ps?
On Mon, Jan 27, 2014 at 3:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/27/14, 3:49 PM, shivangi nangia wrote:
>> As I had explained earlier, I have done MD at varied protein bi-layer
>> I now want to create a probability distribution histogram along the
>> coordinate I generated by varying the distances.
>> I know I can concatenate various .trr files I have from various MD runs
>> 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
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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