Hello Charles and others, We want to implement a custom potential for an ensemble based simulation. While implementing the methods I have some questions and would want to clarify that.
This is a long email and I apologize for the length but I tried my best to keep the questions clear. The potential I am writing is a very simple one : This potential does not compute any energies or changes the derivatives. It simply updates the alignment tensors of RDC's and the weights assigned to individual members of the ensemble. [We want to test something apart from the pseudo-atom approach implemented in XPLOR]. I am attaching a very simple skeleton class of the custom potential. Question 1: How to obtain the instantaneous atomic co-ordinates of the members of the ensemble ? Answer (please confirm) : * esim.members(memberIndex).atomPosArr() would contain the instantaneous atomic positions of all the members of the ensemble. Is there an easy way to convert cdsVector obtained from that method call to a list? [The documentation says a slice of [:] would do it but in my case it resulted in another cdsVector. * * * * Question 2: Is there any specified order in which the potentials are computed? Suppose potList is the container for all the potential terms, potList.append(term1), potList.append(term2) are the two potentials added. Is it guaranteed that term1 derivatives and energy calls are done before term2? This is important because the custom potential should be called before any RDCpots or NOEpots as they would have updated the tensors and weights which would be used by the other potentials * I have tried to use analyze(potList) but I think that sorts the energy terms in alphabetical order before computing energies. Question 3: I do not want XPLOR to compute alignment tensors as the custom potential does it. So would a statement like configIVM_fixDa(rdc.oTensor,engine) [fixRh] ensure that? Essentially I want to skip XPLOR's alignment tensor computation but change the alignment tensors by the custom potential. Apologies again for a lengthy mail. Thanks for your patience, Santhosh * *
customPot1.py
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