It's not clear whether you are reporting single points or post-equilibration time averages, but either way you must expect differences. MD simulations are chaotic. However, the long-time ensemble averages should agree well - that's the point of the simulation.
Mark On Wed, Sep 11, 2013 at 10:35 AM, Xu, Jianqing <x...@medimmune.com> wrote: > Dear all, > > This is my first time here. I apologize if I am not aware any rules for > posting a new message. > > I was testing Gromacs on two servers, one server has AMD Opteron processor > (Server 1), and the other has Intel Xeon processor (Server 2). The simulation > system that I tried is the lysozyme system from the online tutorial > (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/). > Briefly, it has a lysozyme in 10824 water, and 8 Cl-. Box size is around 6.99 > nm. > > I finished all the preparation steps advised by the tutorials, and tested the > final NPT production runs on two servers, using the same final input file > "md_0_1.tpr". It is strange that the results from Server 1 (AMD) has higher > potential energy than the results from Server2 (Intel), specifically, results > from Server1 (AMD) has higher "Coulomb-(SR)" than Server2 (Intel) ( ~ > -5.5*10^5 .vs. ~ -5.7*10^5 kj/mol ). > > I was wondering if anyone could give me any suggestions about what could be > the reasons causing this discrepancy. > > Some additional information: > 1). Jobs run on my local computer, which also has Intel CPUs (Intel(R) > Xeon(R) CPU E5620 @ 2.40GHz), reported the same results as the Server2 > (Intel(R) Xeon(R) CPU X7550 @ 2.00GHz). > 2). All installations (Gromacs and OpenMPI) on Server 1 and 2 were compiled > independently, but with the same arguments. > > > I understand that the information I provided may not be sufficient. If I > should provide more specific information, please let me know. > > Any help will be highly appreciated! > > Thanks, > > Jianqing > To the extent this electronic communication or any of its attachments contain > information that is not in the public domain, such information is considered > by MedImmune to be confidential and proprietary. This communication is > expected to be read and/or used only by the individual(s) for whom it is > intended. If you have received this electronic communication in error, please > reply to the sender advising of the error in transmission and delete the > original message and any accompanying documents from your system immediately, > without copying, reviewing or otherwise using them for any purpose. Thank you > for your cooperation. > -- > 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
