Hello Santhosh-- > > 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].
Well, if you want to evaluate an energy based on RDCs, you will need to evaluate a gradient. I think you want a modern implementation of Sass, H.-J., Musco, G., Stahl, S.J., Wingfield, P.T., and Grzesiek, S., ``An easy way to include weak alignment constraints into NMR structure calculations", J. Biomol. NMR 21, 275-280 (2001). > > 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. > You can get a list by calling list(esim.members(memberIndex).atomPosArr()) > 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 They are evaluated in the order in which they are added. > > I have tried to use analyze(potList) but I think that sorts the energy terms > in alphabetical order before computing energies. It sorts the terms before printing output. > > 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. You really want to get rid of the pseudo atoms as they will serve no purpose in your potential term. best regards-- Charles _______________________________________________ Xplor-nih mailing list Xplor-nih@cake.cit.nih.gov http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
