[gmx-users] Gromacs on Intel Xeon and AMD Opteron

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 11 11:56:32 CEST 2013

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


On Wed, Sep 11, 2013 at 10:35 AM, Xu, Jianqing <xuj at 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
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