AW: NAMD 2.8 and PLUMED 1.3

From: Norman Geist (
Date: Mon Sep 03 2012 - 01:34:07 CDT



what is the output of the patching command? What version of awk do you have

And what is likely more important, does the compilation works without the


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Freitag, 31. August 2012 20:58
An: candy deck
Betreff: Re: namd-l: NAMD 2.8 and PLUMED 1.3


this sounds like a general unix problem. you need to ensure that directory
is included when the compiler is looking for header files. I'm not sure
exactly how this is done, maybe by setting a $INCLUDE_DIR variable in your
shell, or probably there is something you can add to the compile line, for
instance ./build [your stuff here] -I [directory where that file is].

Anyway, I think it's a simple enough problem, just needs some googling or
someone with more unix experience than me.


On Thu, Aug 30, 2012 at 8:59 AM, candy deck <> wrote:



Dear NAMD user.
I'm trying to install NAMD 2.8 and patching PLUMED1.3
Here is what I've done :

tar xzf NAMD_2.8_Source.tar.gz
  cd NAMD_2.8_Source
  tar xf charm-6.3.2.tar
  cd charm-6.3.2

Build and test the Charm++/Converse library (network version):
  ./build charm++ net-linux-x86_64 --no-build-shared --with-production
  cd net-linux-x86_64/tests/charm++/megatest
  make pgm
  ./charmrun ++local +p4 ./pgm (also try running on multiple nodes)
  cd ../../../../..

Download and install TCL and FFTW libraries:
  tar xzf fftw-linux-x86_64.tar.gz
  mv linux-x86_64 fftw
  tar xzf tcl-linux-x86_64.tar.gz
  mv linux-x86_64 tcl

Set up build directory and compile:
  network version: ./config Linux-x86_64-g++ --charm-arch net-linux-x86_64
apply the patch: ./ -patch

  cd Linux-x86_64-g++

And here, things like :
src/ComputeMgr.C:83:21: fatal error: metadyn.h: No such file or directory
compilation terminated
are showing up...

However, metadyn.h exists...
if I do ls -l , I obtain :

lrwxrwxrwx 1 candy candy 36 2012-08-30 13:55 metadyn.h ->

Can someone help ??
Thanks a lot

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:29 CST