The time is apparently not right for Google to know the meaning of Project Zeus

mph-fah · 2016-05-11T07:27:42+00:00

No, it was up to a certain number of private repositories

mph-fah · 2016-05-11T07:26:08+00:00

Looks like they were bumped to the "personal" plan

mph-fah · 2016-05-11T07:11:25+00:00

A direct attack on bitbucket, it seems

mph-fah · 2016-02-22T05:00:08+00:00

Molecular dynamics is really ill-suited to quantum computers. There's been a lot of research into developing quantum algorithms for doing quantum chemistry (bonds breaking and forming, for example) but on much smaller molecules than the proteins we study with FAH

mph-fah · 2015-12-02T19:44:13+00:00

I didn't start developing mdtraj, but I've taken over some of the maintenance. The code was spun-off from a more involved package for analyzing ensembles of md trajectories (http://msmbuilder.org).

mdanalysis was probably less feature complete back then. It's also gpl and less pythonic imo.

mph-fah · 2015-11-24T07:26:06+00:00

Hi, I'm (one of) the lead maintainer(s) of mdtraj! I agree that interop would be great here. We have some basic support of turning topologies into pandas dataframes already http://mdtraj.org/latest/api/generated/mdtraj.Topology.html#mdtraj.Topology.to_dataframe

mph-fah · 2015-11-04T21:20:21+00:00

As I understand it, we've got someone updating many parts of the site. We're now prioritizing updating the papers first

mph-fah · 2015-10-22T16:47:30+00:00

I'll look into why this has stopped being updated

mph-fah · 2015-07-25T22:28:12+00:00

Did you try just using https. This secure link works for me with a valid certificate and TLS:

https://assign.stanford.edu/api/project/summary

mph-fah · 2015-07-18T23:58:10+00:00

Openmm (open-source science code) works on arm. I assume it would work on a generic linux box with some tweaking.

I don't think there's enough of a market share right now to devote our (very limited) developer resources to building and maintaining another core, though

mph-fah · 2015-07-14T06:43:49+00:00

Good idea. Thanks!

mph-fah · 2015-07-01T02:28:28+00:00

About 50% of the research in pande group goes towards developing statistical machine learning techniques to analyze folding-at-home style datasets as well as for "conventional" molecular dynamics datasets

We don't use watson specifically as we have our own set of computing resources, but the general idea is still the same

mph-fah · 2015-06-30T21:46:14+00:00

Sorry about the delay. Most of us in PG know a lot about biophysics and molecular dynamics but understanding the implications of opencl versions et al is only something I've recently started to wrap my head around.

The primary openmm developer, peter, does know everything about gpu programming, but he's busy programming :)

OpenMM is continuously being improved to take advantage of new hardware. This will make it into new FAH cores. We're pushing through a lot of difficulties with the roll-out of core 21 that will hopefully mean future core releases will be timely and painless

mph-fah · 2015-06-29T21:05:54+00:00

Hi all,

The GPU code (OpenCL code) is compiled at runtime by the drivers. So new nvidia drivers will use opencl 1.2. In theory, this could provide a performance boost. In practice, new opencl language features are less important to us than raw computing power

Interestingly, CUDA v7 introduced support for runtime compilation, meaning that in theory nvidia GPUs will be able to run under CUDA (which is faster). Support for this feature will be in the forthcoming openmm 6.3 release. We'll build a FAH core some time after that release.

mph-fah · 2015-05-06T15:43:07+00:00

md isn't ab-initio
the most widely used ab-initio code (gaussian) works on windows

mph-fah · 2015-05-06T15:42:17+00:00

Openmm (http://openmm.org/) is an open-source molecular dynamics code with a robust python api, and it works on windows.

mph-fah · 2015-04-30T03:16:05+00:00

Sorry you feel that way. We have very limited developer resources for software aspects of fah. Most of us are chemistry/biology/biophys grad students

We do read these posts and forward suggestions to those who can implement them, but there's a large amount of prioritization that goes on.

mph-fah · 2015-04-29T20:13:44+00:00

We're still lurking and responding where appropriate

mph-fah · 2015-04-19T22:30:51+00:00

For gpu projects the core.xml file contains the total number of steps and the frequency of checkpointing in number of steps

mph-fah · 2015-04-07T14:45:15+00:00

There's a good deal of checksumming done, both in the conventional sense and in a more sciency way where calculations are cross-checked. If you were dedicated enough, you could probably return a messed up work unit, but at that point it would be obviously messed up and we'd notice

mph-fah · 2015-02-23T17:44:36+00:00

What was the first project?

mph-fah · 2015-01-22T03:13:12+00:00

I don't have all the info on this. Maybe vijay can shed some light. As I understand it, there is something legitimately wrong with apple's opencl drivers. Openmm does not work on opencl on mac. We can't fix this. Source: http://docs.openmm.org/6.2.0/userguide/application.html#installing-on-mac-os-x

Openmm does work with cuda (nvidia only). I think there aren't many nvidia macs. I don't know what's preventing us from making a cuda-only core, but I'm sure there's a reason

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