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869 discussions

RMSD between sets of particles
by Davide Baù 11 Dec '13

11 Dec '13

Hi, is there a way of getting the RMSD between two set of particles (not atoms)? I'd like to create a score based on the RMSD between two models in order to decide when to stop a Molecular Dynamics (or Brownian Dynamics) simulation. Thanks, Davide

2 1

changes to RMF format
by Barak Raveh 25 Nov '13

25 Nov '13

Hi Daniel, can you give a quick informal description of the main updates in the format of the new RMF and the major interface changes (or point me to a doc where those exist). I would like to try to hack things to work for the npc with cimera, but will need help with getting started :) Cheers! Barak

3 2

randon number generation on GPUs
by Barak Raveh 18 Nov '13

18 Nov '13

Hi, has anyone experimented with using the GPU to accelerate random number generation in IMP simulations - something along the lines of: http://arxiv.org/abs/1204.6193 http://www.sciencedirect.com/science/article/pii/S0021999111003329 Thanks! Barak

1 0

adding periodic boundary conditions?
by Barak Raveh 15 Nov '13

15 Nov '13

I am considering the addition of periodic boundary conditions support to the BD simulation. I guess it would apply to any optimizer in IMP - what would be the technical complications? I guess naively,what is needed is mainly to reformulate the restraints in a periodic way, but I wonder if it affects any sort of score evaluator optimizations (ClosePairs, etc. - the latter is probably easy to handle as it mainly affects particles at the boundary). In the future it will also allow periodically optimized restraints (such as ones using FFT). Barak p.s. in my particular case, I thought of PBC over the x,y plane only, if that matter for anything, which I believe it doesn't

3 6

MD and WLC functions
by Davide Baù 14 Nov '13

14 Nov '13

Hi, I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. Are they safe to use? Thanks, Davide

2 18

clang-format and autopep8
by Daniel Russel 08 Nov '13

08 Nov '13

My recent favorite coding tools are clang-format and autopep8 that do auto-formatting of C++ and python code respectively. They are pretty easy to set up on a mac given homebrew and access to easy_install. Using them results in nicely formatted python and C++ code with little effort. I put some instructions at < https://github.com/salilab/imp/wiki/Code-formatting>.

1 0

2.1 release, last call
by Daniel Russel 21 Oct '13

21 Oct '13

Assuming there are no hiccups with today's doc changes tonight, I'd propose we declare the current state of IMP to be the release (see the develop branch or the release/2.1 branch). Anyone who hasn't run their code on IMP from the last week or so (it hasn't changed significantly in that period) is highly encouraged to do so to make sure some recent fixup hasn't broken anything.

5 10

2.1 release branch created
by Daniel Russel 15 Oct '13

15 Oct '13

I created the 2.1 release branch (release/2.1). It would be nice if anyone who hasn't updated in a while checks it out and makes sure there stuff works with it. To check it out do `git imp update` `git checkout -b release/2.1 origin/release/2.1` then build. An issue I just discovered is that the version number support got broken along the way, so you version number will be wrong. I'll fix that shortly.

2 2

IMP 2.1 release
by Daniel Russel 11 Oct '13

11 Oct '13

Seems like things are basically ready for the 2.1 release. Tests last night were good and the two open issues on the 2.1 milestone haven't changed recently and seem like we can let them slide (they won't, I think result in significant API or functionality changes). For reference they are: - dock with crosslinking being broken: https://github.com/salilab/imp/issues/560 - compilation warnings in ISD: https://github.com/salilab/imp/issues/539 There will be a 2.1.1 release pretty soon if necessary anyway. Since there were a couple of commits today, I'll check that nothing breaks in the tests run tonight and if not, create the release branch tomorrow.

1 0

IMP 2.1
by Daniel Russel 01 Oct '13

01 Oct '13

It is time to start on the 2.1 release. There are currently two issues open in the tracker attached to that milestone - one regarding isd (#526) - and the MC mover/optimized behavior. I'd like to resolve the latter by adding checks so errors are thrown with most movers if they try to move non-optimized attributes, which should be a relatively quick change that I can do this afternoon. Otherwise, is there anything else that someone thinks should be cleaned up before the release?

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