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
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