Hi,
I got both the MD and the BD to work, but there is something I don't understand about the wlc.
If I set it up and like this (with both MD and BD): > l_max = 100.0 > lp = 5.0 > wlc = IMP.misc.WormLikeChain(l_max, lp) > sd = IMP.core.SphereDistancePairScore(wlc) > crw = IMP.container.PairsRestraint(sd, cpc) > crw.set_weight(kforce) > m.add_restraint(crw)
And then check the l_max and lp values with: > sl_max = wlc.evaluate_with_derivative(l_max) > slp = wlc.evaluate_with_derivative(lp) > print "l_max %f\nlp %f" % (sl_max[0], slp[0])
I get "out of scale" values, even if wlc is the only score applied, e.g.: > l_max 590.102905 > lp 0.022517
Another thing that I noticed is that, apparently, only l_max has a influence on the final structure (it constrains the occupancy). Is that expected?
Thanks, Davide
On Nov 11, 2013, at 11:07 PM, Daniel Russel wrote:
> Or just not marking the particles as optimizable? At least if you use a thermostat, things should move even with no forces. It is a bit confusing (making sure particles are optimized).... You can also pass the list of particles to be optimized explicitly to the optimizer, I kind of prefer that way. > > > On Mon, Nov 11, 2013 at 7:18 AM, Davide Baù davide.bau@gmail.com wrote: > Ah! > I think I was missing the forcefield (particles were not being optimized). > > > > On Nov 11, 2013, at 4:16 PM, Daniel Russel wrote: > >> What aspect of MD would you like an example of? The MD class basically has two functions: one to set the time step and one to optimize. For the force field side there are already the charmm_forcefield examples. The bencmark_md_charmm.cpp provides a pretty simple example of using them together. >> >> >> On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote: >> Thanks Daniel! >> >> Could you please provide a MD example too? >> >> Davide >> >> >> On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: >>> Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing. >>> >>> >>> On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: >>> Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? >>> I'm asking because the code works with existing PairScores, but they are mainly distance scores. >>> >>> Davide >>> >>> >>> >>> >>> >>> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >>> >>>> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). >>>> >>>> >>>> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >>>> That would help, thanks! >>>> >>>> >>>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>>> >>>>> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >>>>> >>>>> >>>>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>>>> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >>>>> >>>>> Davide >>>>> >>>>> >>>>> >>>>> >>>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>>> >>>>>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>>>>> >>>>>> On Monday, November 4, 2013, Davide Baù wrote: >>>>>> Thanks Daniel! >>>>>> >>>>>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>>>>> >>>>>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>>>>> 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 >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>>> >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev