I was trying to assign markers to a skinned mesh to simulate collisions but the marker doesnt follow the skinned meshes form. Its rigid and just stays in the origin. Is there any way of adding collisions to a skinned mesh or cloth sim so that that the ragdoll collides with the mesh? Im still really new to Ragdoll Dynamics so any help would be greatly appreciated!
Hi @Nithin_Piano, welcome to the forums! 
Unfortunately, Ragdoll does not support deforming meshes. So it will only respect a mesh as it is when you replace the mesh. If you have History enabled in the Option dialog, it will respect changes made at the start frame, but will not deform over time.
The typical solution is to apply Markers to the skeleton of your character and adjust these to follow along with the rig.
If you have an example of what it is you are trying to do, I may be able to provide more tips and tricks.
Thank you so much for the quick response Marcus! I made a davy jones rig and was adding ragdoll to the tentacles. Needed a way for the tentacles to collide with the cloth sim on the body. But I think i can add the markers to the joints of the body and adjust them from there. Thanks again!
Very cool, that’s a very good usecase for Ragdoll. The tentacle animation would be transferred into the sim, whilst preserving contacts and momentum. Should look really good. Please do share anything you come up with if possible! 
So I ended up duplicating the shirt mesh, Contraining it to the root joint and then adding a marker so that the marker kind of takes the shape of the mesh. it kind of works for the scene cause its a walk cycle rig test. Will surely share the end result with ya! This plugin is literally a lifesaver!
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Hey Marcus so I used ragdoll for the tentacles. So far I’m over the moon with the results!
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Very cool @Nithin_Piano, thanks for sharing!
For a next step, can I suggest adding some animation onto the assigned tentacles? E.g. 5 degrees of Rotate X over 25-50 frames in a loop? The dynamic tentacles would then squirm and create knots amongst each other, just like in the movie!
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Thank you!
I actually did add individual animations to the tentacles but because of the gravity and the motion of the entire body, they were hard to notice. I reduced the baked animation layer weight too but thats as far as I could get them to curl without making the sim look weird. I think I need to play with the settings a bit more to get them to follow the animation. Would really appreciate any tips for getting the ragdoll to follow the animation closer. Thanks so much for your time!
If you can share what happened when it started to look weird, I might be able to give some pointers. Generally, the higher the Rotate Stiffness the closer it’ll follow your animation. You may also need to lower Rotate Damping.
So when i decreased the animation layer weight, the animation started to glitch at certain points, prob cause the base animation and the sim animation layer were at odds with each other .
Ah gotcha I thought adding more rotate stiffness would make the tentacles too stiff. But i get your point with decreasing rotate damping at the same time as increasing rotate stiffness. I still have to experiment with this alot so ill definitely keep you posted!
Staying loose and following your animation are opposites; the stiffer the simulation, the closer it follows your animation and vice versa.
Do you mean you are decreasing the layer weight on a recorded physics simulation? That could cause intersections to occur, since Maya’s layers do not know about contacts the way Ragdoll does. You’d be better off increasing stiffness to remain close to the animation, and playing with damping until you get the effect you are looking for.
Yep I was under the impression that inreasing stiffness would make the ragdoll sim more rigid. I couldnt do any tests recently but will definitely give this a shot.
Yeah I reduced it to around 70% and obviously the intersections were bad but not that noticable so I kinda left it in. Definitely gonna add more stiffness and fix it this way. This will help alot with the final animation. Thanks so much!