Date: Tue Jul 13 2010 - 23:08:57 CDT


Correct me if i am wrong, but i think when you say topology you actually mean the forcefield parameters.
Sure you can. You can obtain a probability distribution from an all atom simulation for any feature of a set of degrees of freedom. Then using the relationship p(x) = exp (-V(x)/kT), where V(x) is the potential you can obtain new ad hoc parameters.

take a look at the nanodisc papers where the parameters set that comes with VMD where obtained.



----Mensaje original----


Fecha: 13-07-2010 03:42

Para: "namd-list"<>

Asunto: namd-l: RBCG


Hello.If i am not wrong, u can add new information to your topology file using paratool on vmd and QuantumMechanical simulatios as a base.Is there a way to add new information to my CG topology file using all-atom simulations as a base?(i use the RBCG method)

thank u,Dota.

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