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-- Francesco Gentile PhD Student, Biophysics CCIS 3-215, Department of Physics 7-112, Li Ka Shing Centre for Health Research Innovation University of Alberta, Edmonton, AB T6G 2E1 Canada On 24 Mar 2016 5:19 p.m., "Francesco Gentile" <fgentile.ualberta.ca> wrote: > Thanks very much. I realized later I was fitting to a single atom, > obtaining consequently zero. I modified my script but I still have > problems. basically the ion rmsd is reasonable but in some points it jumps > to weird values such as 80+ angstroms, to return at the normal value after > a while. I think there is something wrong in my script affecting the > centering or something like that. My new script is > > trajin.. > > image origin center familiar > > rms first mass out rms_back_bgw.dat ':1-132.CA,C,N' time 2.0 > > rms first mass ':34,44' (I used this option to fit on the coordinating > residues after the first trials but it does not change the weird behaviour) > > rms first mass out rms_mg_bgw.dat ':133.MG' time 2.0 nofit > Again, the MD trajectory looks normal. Any suggestion? thanks in advance > -- > Francesco Gentile > PhD Student, Biophysics > CCIS 3-215, Department of Physics > 7-112, Li Ka Shing Centre for Health Research Innovation > University of Alberta, Edmonton, AB T6G 2E1 > Canada > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Mar 25 2016 - 12:30:07 PDT