[gmx-users] binding_affinity

[Justin A. Lemkul]

shahid nayeem wrote:
> Hi Justin
> Before trying for my system I am trying to learn running these
> simulation with the help of your tutorial. The only change I made is
> that I applied pull_code for 2nm movement only in order to save time.
> Thereafter, with trjconv I generated all 200 conf.gro. when I run your
> perl script it does gives an oitput of summary_distance.dat. It has
> one column of conf.gro number but no distance. Where I am wrong.

I don't know exactly, but the script runs 500 iterations of each calculation, so 
you may have 200 lines of content then 300 incomplete lines, unless you've 
properly modified the script.

-Justin

> Shahid Nayeem
> 
> On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Justin A. Lemkul wrote:
>>>
>>> shahid nayeem wrote:
>>>> Hi Justin
>>>> Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
>>>> mimicking physiological condition.
>>> More of a hybrid of physiological and in vitro conditions.  Please see the
>>> referenced paper for more details.
>>>
>> ...and again, please don't necessarily conclude that just because someone
>> did this for a tutorial that you should inherently be doing it for your
>> system.  The tutorial is but one example of a workflow, derived from my own
>> specific work. Construct a model that is most appropriate to your purposes.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================