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

shivangi nangia shivangi.nangia at gmail.com
Tue Jan 28 02:29:41 CET 2014


I see this when I run g_analyze command:

SS1   6.104595e+00   5.846878e-01   2.386978e-02      -0.151   -0.227
SS2   8.228340e-01   3.035145e+00   1.239093e-01      -0.283   -0.417
SS3   6.970040e-01   3.047464e+00   1.244122e-01      -0.347   -0.411
SS4  -4.231055e+00   2.099952e-01   8.573016e-03      -0.191    0.047

these are 4 sets.

I think the & separates these 4 sets.

What is the significance of these 4 sets, what is it telling me?

Thanks,
sxn



On Mon, Jan 27, 2014 at 8:13 PM, shivangi nangia
<shivangi.nangia at gmail.com>wrote:

> 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
>> 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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