Hmm, that looks like a problem. Which GROMACS version, and which compiler version? (See mdrun -version)
On Wed, Sep 11, 2013 at 3:06 PM, Xu, Jianqing <x...@medimmune.com> wrote: > > Thanks for the comments, Mark. > > Sorry that I did not explain my question clear enough. > > I am actually talking about post-equilibration time average. I understand > that some instantaneous deviations are expected, but the simulations should > be correct as long as the ensemble averages are the same (or close enough), > but the differences that I observed seemed beyond that. > > I firstly realized the total energy reported from two servers are obviously > different (again, two simulations started from the same *.tpr file, and the > executable on each server were compiled independently using the same > arguments). I then checked the potential energy and kinetic energy as shown > the below link: > > https://docs.google.com/file/d/0B7MGQ6N_2Ln7emRySENsZU40d2s/edit?usp=sharing > > > Looks like the differences are from the potential energy. I then took a quick > look at the LJ (SR) and Coulomb (SR) components, and it looks like the > Coulomb (SR) component has big deviation which beyond the numerical errors. > There are other differences, but looks like the Coulomb (SR) is the most > obvious one. I was not able to understand how this can happen. > > https://docs.google.com/file/d/0B7MGQ6N_2Ln7bzB4YVhvMjdsNkE/edit?usp=sharing > > I hope the figures can clarify my situation better, and I will appreciate if > you or anyone else on the list could provide more suggestions. > > Thanks a lot! > > Regards, > > Jianqing > > > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Mark Abraham [mark.j.abra...@gmail.com] > Sent: 11 September 2013 10:56 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Gromacs on Intel Xeon and AMD Opteron > > 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. 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