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 Bał <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 Bał <davide.bau@gmail.com> wrote:
Thanks Daniel!Could you please provide a MD example too?DavideOn 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 Bał <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.DavideOn 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 Bał <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 Bał <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.DavideOn 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 Bał 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 Bał <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
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