[no subject]

One of our systems is the G-Protein Coupled Receptor CB1 immersed in a 
lipid bilayer that is solvated with water.  I think we have around ~50K 
atoms in the simulation.  It looks visually like a cube with three 
layers.  The water layers are on both sides of the lipid bilayer 
solvating the phospholipid headgroups.  You can go to 
<a  rel="nofollow" href="http://www.lipid.wabash.edu/";>http://www.lipid.wabash.edu/</a>, which is Dr. Scott Feller's homepage, to 
get an idea of what a similar system looks like.  He is working on lipid 
bilayer simulations containing the GPCR in your eye that responds to 
photons called Rhodopsin.
Dow

Joe Knapka wrote:
&gt;Dow_Hurst &lt;dhurst at mindspring.com&gt; writes:
&gt;
&gt;[snip]
&gt;
&gt;  
&gt;&gt;Just to pass on some good news: The cluster is Opteron 250 CPUs in
&gt;&gt;dual CPU 1U configuration.  We have 19 slave nodes and one head
&gt;&gt;node.  The switch we have is a SMC 8624T.  The special fast
&gt;&gt;interconnect is the Ammasso GigE RDMA 1100 NIC.  Using the molecular
&gt;&gt;dynamics package NAMD, I've found that with the NAMD benchmark input
&gt;&gt;file of ~92K atoms, the apoa1 protein, that we can get using Ammasso
&gt;&gt;MPI libraries a full nanosecond of simulation time in 0.96 days.  If
&gt;&gt;I try to scale up using just standard TCP communications and not use
&gt;&gt;the Ammasso MPI, we can do a full nanosecond in 1.31 days.  What
&gt;&gt;this means is that with our smaller cluster of 19 nodes we are still
&gt;&gt;benefitting very well using the fast interconnect from Ammasso.
&gt;&gt;When you think that we will save 462 minutes per nanosecond
&gt;&gt;simulation time and we need a lot of nanoseconds to actually see
&gt;&gt;changes, the fast interconnect shows it's worth.
&gt;&gt;    
&gt;
&gt;Holy cow. How does one test such a system? I mean, it would suck to
&gt;simulate a couple of hundred nanoseconds, only to find that you're
&gt;getting bogus results. I'm trying to imagine how the developers of
&gt;NAMD validated their code. Are there simpler problems that one
&gt;can simulate much more quickly?
&gt;
&gt;Also, I wonder how well your performance will scale with additional
&gt;CPUs?
&gt;
&gt;-- Joe Knapka
&gt;_______________________________________________
&gt;Ale mailing list
&gt;Ale at ale.org
&gt;<a  rel="nofollow" href="http://www.ale.org/mailman/listinfo/ale";>http://www.ale.org/mailman/listinfo/ale</a>
&gt;
&gt;  



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