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 <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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists