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[ale] Syntax problem

Most of the time people don't try to go beyond 10 nanosecond 
simulations.  It has been just too time consuming.  Now, with faster 
cheaper Linux clusters much longer simulations are becoming within 
reach.  Your right though, about several hundred nanoseconds in a bad 
simulation being not a good thing!  Applying all known good experimental 
data to your simulation initially helps keep the simulation within 
reality.  Too many simulations are setup from the get go without every 
bit of good data being applied.  It all goes back to knowing the 
literature and being able to separate the good data from poor data.  You 
have to apply what you can to keep the simulation from being out there 
in la la land.

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 
http://www.lipid.wabash.edu/, 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.

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