[gmx-users] Different results from identical tpr after MD
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 5 20:41:25 CEST 2012
bipin singh wrote:
> Thanks for the reply.
> / /I read the link. So, how one can predict something reliable using
> these results(based on 50ns in my case) which changes on different
> machines? which depends more on the environment of the computer
> architecture and other variables of mdrun rather than system
> (Protein/DNA/RNA) itself for a short simulation, where we don't have
> enough resources to run infinitely long simulation.
No one can do anything for an infinite amount of time ;) Hence replicate
simulations and thorough statistical analysis are required to obtain reliable
results and prove that what you've done is to be trusted. The other comments in
this thread are quite good so I won't recapitulate other points that have been made.
> And also how to believe the statement made by several research papers
> based on unconverged simulations.
I wouldn't trust any conclusions drawn from demonstrably unconverged
simulations. Not everything that's published has been done correctly. Peer
review is an imperfect system, so be careful what you read and apply good
> On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> bipin singh wrote:
> Hi all,
> I am really surprised to see different results from two
> identical md simulation. I have used identical tpr files for the
> mdrun (for 50ns) and after the completion of the md job I found
> that the results from the identical runs is totally different.
> To further confirm this, I have converted both the input tpr to
> mdp using gmxdump and diff the two files and found that the mdp
> is identical.
> Please let me know what can be the reason of this behaviour. I
> know that it is unexpected and even I can't believe how can it
> be possible.
> It is not unexpected at all. Please consult:
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> Bipin Singh
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users