[gmx-users] reproducibility of trajectory

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 19 11:32:34 CEST 2015


You've observed a single event. By itself that doesn't mean much of
anything. If you were in a car crash today, that doesn't mean you will be
in one every time you go on the road. But if you observe yourself in a car
crash every day, now you have evidence that you need driving lessons... If
you had a car crash once every hundred days, and reported only that single
day as evidence you need lessons... that'd be wrong on many levels.


On Wed, Aug 19, 2015 at 10:31 AM Qing Lv <lvqingjiejie at 163.com> wrote:

> Hi,
> I did a 200-ns MD for a protein and found an interesting conformation
> transition, and according to NMR study in literature, it is believed that
> 10 us ~ ms scale simulations are needed to get this conformation transition.
> However, when I tried to reproduce this conformation transition, I was not
> so lucky any more... I repeated 6 x 200ns trajectories but failed to
> reproduce, even I used the same seed number.
> Do you have any ideas on this? Is it sufficient to present this result in
> papers, since I just got 1 trajectory?
> Thanks,
> Qing
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list