**From:** Ivan Gregoretti (*ivangreg_at_gmail.com*)

**Date:** Tue Jul 22 2014 - 07:33:14 CDT

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Hi Jérôme,

Could you expand your answer a little bit?

Thank you,

Ivan

On Tue, Jul 22, 2014 at 7:56 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*> That is completely dependent on what variables you define, how many atoms
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*> are involved, and the biases.
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*>
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*> Jerome
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*>
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*>
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*>
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*>
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*> On 22 July 2014 13:27, George Patargias <gpat_at_bioacademy.gr> wrote:
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*>>
*

*>> Hello,
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*>>
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*>> I am comparing the Benchmark times for a given system (~258,000 atoms)
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*>> using
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*>> NAMD_CVS-2014-06-02_Source version with and without the colvar module on.
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*>>
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*>> When the colvar module is *off* (equilibrium MD), I get something like
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*>>
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*>> Benchmark time: 256 CPUs 0.0268481 s/step 0.155371 days/ns 540.59 MB
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*>> memory
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*>>
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*>> When the colvar module is *on* (moving harmonic restraint on an RMSD
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*>> colvar calculated from 1981 C-alpha atoms), I get
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*>>
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*>> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns 569.555 MB memory
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*>>
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*>> which is 11-12 times slower.
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*>>
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*>> Is this the actual computational cost of a colvar calculation?
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*>>
*

*>> Also the scaling of this particular colvar calculation is not good:
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*>>
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*>> Benchmark time: 48 CPUs 0.331787 s/step 1.92006 days/ns
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*>> Benchmark time: 128 CPUs 0.322472 s/step 1.86616 days/ns
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*>> Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns
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*>>
*

*>> Thanks in advance!
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*>>
*

*>> George
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*>>
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*>> Dr. George Patargias
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*>> Postdoctoral Research Fellow
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*>> Biomedical Research Foundation
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*>> Academy of Athens
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*>> 4, Soranou Ephessiou
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*>> 115 27
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*>> Athens
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*>> Greece
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*>>
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*>> Office: +302106597568
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*>>
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*>
*

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