Re: Compiling NAMD 2.7 with the PLUMED patch

From: Davide Branduardi (davide.branduardi_at_gmail.com)
Date: Thu Jan 06 2011 - 17:42:56 CST

Hi Gianluca,

My guess is that something went wrong while patching namd with plumed.
(did you see if any hunk failed?)
Probably the best place to discuss this is on the plumed mailing list, please provide details,
especially about your input and the outputs in the patching procedure and we'll do our best to help you.
BTW in the plumedpatch there are probably a couple of things that you need to set, namely:

# this can be set up with an environment variable
plumedir="the/directory/containing/plumed"
# USER DEFINED ARCHITECTURE:
myarch="Linux-x86_64-g++"

Good Luck

Davide

**************************************************************
Davide Branduardi
Post Doc- Computational Chemistry
Drug Discovery and Development
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy

On Jan 6, 2011, at 11:55 PM, Gianluca Interlandi wrote:

> Hi!
>
> Does anybody have experience compiling NAMD 2.7 with the PLUMED v1.2.2 patch? I have followed the directions:
>
> 1) build charm++ converse library: ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production
>
> 2) Configure NAMD code: ./config Linux-x86_64-g++ --charm-arch net-linux-x86_64
>
> 3) apply the patch: ./plumedpatch_namd_2.7.sh -patch
>
> 4) compile NAMD as usual: cd Linux-x86_64-g++ ; make
>
> NAMD compiles correctly and the alanine benchmark runs fine.
>
> However, when I try to run one of the PLUMED tests in the PLUMED package, I get the error:
>
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: plumedfile
> ERROR: plumed
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
> It looks like as if the PLUMED patch did not work. Can anybody with experience compiling NAMD+PLUMED please help me?
>
> Thank you very much!
>
> Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>

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