simtk.org

The system i am trying to simulate consists of 7 nucleotides GGAAACU. The terminal nucleotides are set to rigid using the command "basepair" and overall bond mobility is set to Free using "overallBondMobility". At this point, i am interested in setting the bond mobilities of the
2nd G to Torsion. Since the basepair command does not support this feature, i inserted a line
(static_cast<RNA&>(myMolecule[0])).setRNABondMobility(BondMobility::Torsion,1,1);
in the function constrainedDynamics::runDynamics() in Repel.h. This seems to be working fine in the sense that the constraint forces i obtain from the function calcMobilizerReactionForces are non-zero for
the locations corresponding to nucleotide number 1 (2nd G).

However the bond mobility between the O3*-C3* and C3*-H3* has been set to rigid. The function getAtomMobilizedBodyIndex returns the same
value for all these three atoms belonging to that nucleotide. I am not sure why this is happening.

Also, is there a better way to achieve the kind of mixed bond mobilities that i am looking for ? Terminal nucleotides are rigid, AAAC are fully atomistic and the second G has torsional bondmobilities ?

Regards,
Kishor Bhalerao

sorry again to be responding to an ancient post.

this sounds odd. I think you're doing it correctly. If you're still interested, try it again in RNABuilder 2.0 and see if it works.

the syntax has changed, as I think you're aware. let me know if you need help.