RE: NAMD 2.8 and PLUMED 1.3

From: Buddhadev Maiti (
Date: Fri Aug 31 2012 - 22:40:11 CDT

Dear Candy,

I am going to help you for PLUMED installation. Please let me know how are you going to install: one node multiple processors / multiple nodes multiple processors

Have a nice weekend,

From: [] on behalf of Aron Broom []
Sent: Friday, August 31, 2012 2:57 PM
To: candy deck
Subject: 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 -> ../plumed-1.3/common_files/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 - 23:22:30 CST