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.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 > >