(no subject)

From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Wed Aug 29 2012 - 11:06:10 CDT

Dear NAMD users, I have a question about further analyzing the dcd files. If I want to do extra analysis on the trajectories from a simulation that is not available in the NMAD analysis plugin in the vmd  (for instant in I want calculate average angle resulted for a particular bondangle etc), how should I actually do that. I use to work with lammps and transferring the movie files into the insight format (ASCII format) and do various analysis (density profiles of different groups, rama plots and so on) with my self-written codes. Now I have got a bit problem since I should deal with the binary files...I would appreciate any comment on this please. My other question is about NAMDEnergy plugin. When I try to run it I get the error message that It can not execute the namd2 executable file! this is while I run my simulations with the same file (the namd2). Does anyone know why is this happening? Thanks  Jackie

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