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

[shivangi nangia]

Dear Justin,

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?

Thanks,
sxn


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:
>
>> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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