[gmx-users] binding_affinity

shahid nayeem msnayeem at gmail.com
Thu Apr 21 16:30:20 CEST 2011

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.
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
> 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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