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 <jalem...@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
========================================
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