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.comwrote: >>>> >>>>> 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.comwrote: >>>>>> >>>>>>> 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 > >