AW: Re:

From: Norman Geist (
Date: Thu Aug 30 2012 - 02:32:29 CDT



depending on which kind of analysis you want to do, you can either use vmd
with its own tools and additionally write some tcl scripts, or convert the
dcds to a format your tools can deal with by using the catDCD tool shipped
with namd.


The other error is because a linux system publishes a list of directories
where to search for binarys. So your linux system doesn't know namd2 binary
to provide it to vmd. You can solve this by adding the directory with your
namd binary to the $PATH variable. If you use bash for instance, you can
just do


$> export PATH=/you/namd/dir/:$PATH


Norman Geist.


Von: [] Im Auftrag
von Suranga Edirisinghe
Gesendet: Mittwoch, 29. August 2012 23:14
An: Jacqueline Schmidt
Cc: namd
Betreff: namd-l: Re:


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
<> wrote:

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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