MC steps and MD simulation time

You successfully prepared your system. Now: How do I tell Hippo to produce a trajectory from it? What parameters to choose? And what should I do when things go wrong.
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anmj
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MC steps and MD simulation time

Post by anmj » Tue Aug 26, 2008 12:17 pm

How many MC steps corresponds to 1 ns MD for a protein with 300 residues?

oliver
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Re: MC steps and MD simulation time

Post by oliver » Wed Aug 27, 2008 8:27 pm

That's a very good question. I don't think it has a simple answer.... I am looking forward to further replies :-).

martin
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Re: MC steps and MD simulation time

Post by martin » Fri Aug 29, 2008 7:56 am

We have never tested a system of this size, so it's difficult to answer.

For smaller systems (20-30 residues) we found that one MC scan (i.e. the number of MC moves required to move every residue once) equals to roughly one 2 fs MD time step.

kaihsu
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benchmarking (Re: MC steps and MD simulation time)

Post by kaihsu » Fri Nov 14, 2008 11:28 am

I have a system of 10400 atoms (1293 residues).

I am running Monte Carlo (MC) with implicit membrane with hippo [with Supplemental Streaming SIMD Extension 3 (SSSE3)]. For this, a scan is about 1e4 moves; let’s say this corresponds to a 2 fs molecular dynamics (MD) time-step. The fastest I can get on a Intel Xeon CPU L5410 2.33 GHz processor was 20 moves per second. Running 1e7 steps (? 1e3 scans ? 2 ps) takes ?1 week. (1 ns would therefore take 500 weeks ? 10 years.)

By contrast, I can run an MD simulation with Gromacs of this same system in vacuum on an Intel Xeon CPU 1.7 GHz processor and get 1 ns in 1 day.

Am I being fair here? I wonder whether it is possible to implement parallel MD with implicit membranes, and how fast would that be?

martin
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Re: MC steps and MD simulation time

Post by martin » Sun Nov 16, 2008 1:50 pm

This sounds very slow. What cutoff are you using? With a 14 Angstrom cutoff you should get at least 1000 moves/s on the Xeon.

The MD version of the membrane is implemented and should be much more efficient for larger systems. It still needs a little debugging and probably some form of stochastic dynamics. I will try and do this asap. ;) Definitely before X-mas!

kaihsu
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Re: MC steps and MD simulation time

Post by kaihsu » Mon Nov 17, 2008 4:42 pm

Thanks! I changed the cutoff from 44 Å to 14 Å and am getting about 200 moves per second.

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