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Message boards : News : let's sample the binding site....

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Paola Bisignano
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Message 25991 - Posted: 29 Jun 2012 | 8:57:44 UTC

Hi all,
I am submitting 450 WUs on acemdlong, 53600 credits each.
The group is ADAPT. I want to improve the sampling in the binding region.

Thanks to all for your computing time,

cheers,

Paola

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Message 26030 - Posted: 30 Jun 2012 | 10:40:02 UTC - in response to Message 25991.

Thank you for brining us some new work and your continued efforts at refining your models <applause>

Can you share a little information about what the 4000000 steps represent and how much simulated time this covers?

The WUs I have processed so far in this series have run smoothly.
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Message 26049 - Posted: 30 Jun 2012 | 20:36:54 UTC - in response to Message 26030.

I think GPUGrid gets ~2┬Ás/day, all in.
Many molecular reactions/interactions occur over several microseconds, so a few days crunching by the project can get one model run of several microseconds. Many runs are sometimes needed to get an accurate picture of the interaction, even after refinements.

We have to respect that there is a limit to what researchers can divulge when discussing ongoing work, but it's always interesting to know some specifics about the research, so fill us in any time.
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Paola Bisignano
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Message 26135 - Posted: 3 Jul 2012 | 11:59:35 UTC - in response to Message 26049.
Last modified: 3 Jul 2012 | 12:01:00 UTC

I am running a free ligand binding diffusion simulation. My system is a molecular chaperon and the ligand is a fragment-like compound, so smaller than drug molecules. I need more statistic in the bound region and I am trying to expand the sampling, starting from 45 coordinates snapshots of the complex (ligand-protein).
Sorry I think I cannot say more right now :(


Thanks for your computing time and for your interest on science,

Cheers,
Paola

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Message boards : News : let's sample the binding site....