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-- Yuanhui Tang Doctor Candidate Beijing Key Laboratory for Membrane Materials and Engineering Department of Chemical Engineering, Tsinghua University Beijing 100084, PR China Tel: 86-10-62794742; Email: tangyh08.gmail.com At 2018-06-06 01:13:23, "Wesley Michael Botello-Smith" <wmsmith.uci.edu> wrote: >I would use pytraj to this. You can accomplish the same thing using the " >pytraj.analysis.vector.center" command >see: http://amber-md.github.io/pytraj/latest/_api/pytraj.vector.html >That way you have access to python syntax and you can run your loop in >python. > >You could even then use pytraj.compute or pytraj.pmap if you want to do the >loop for you. These commands can take a python style list of individual >commands as input and will automatically run each one. The pmap command >will even let you run them in parallel. > >If you really want to do this in cpptraj, you would have to write each i j >combination explicitly. Before I learned pytraj, I would usually write a >bash script to generate the cpptraj input script to do that sort of >iteration. > >Hope that helps! > >On Tue, Jun 5, 2018 at 9:53 AM, 唐元晖 <tangyuanhui08.126.com> wrote: > >> Hello all, >> >> >> This is Yuanhui. I want to calculate the distance between two residues as >> :i and :j, and i, j can be changed during a loop. However, the distance >> mask doesn't recognize the word :i. The input file is written like this: >> >> >> parm *.prmtop >> trajin md15.mdcrd 1 last 200 >> i=2 >> j=3 >> distance dist :i :j out dist.dat >> >> >> Is there a way can make the cpptraj recognize the variable 'i' and 'j', >> because I want to change their values. >> Best wishes! >> >> >> >> -- >> >> Dr. Yuanhui Tang >> Ralph E. Martin Department of Chemical Engineering >> University of Arkansas >> Cato Springs Research Center >> Fayetteville, AR 72701 >> email: yt006.uark.edu >> voice: (479) 409-9989 >> >> >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jun 05 2018 - 13:30:03 PDT