From: Suranga Edirisinghe (nerangedi_at_gmail.com)
Date: Wed Aug 29 2012 - 16:13:55 CDT
I think Collective variable analysis tool (PLUMED) will help you.
Please give it a try.
On Wed, Aug 29, 2012 at 9:06 AM, Jacqueline Schmidt <
> 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?
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