Compiling VMD

VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.[1]

Locally-Installed Version

VMD 1.9.1 is installed on Proteus. You must be running an X11 server on your own computer for this to work: Linux should just work, Mac OS X will need XQuartz, Windows will need XMing or similar. It works best over a fast network.

Use the module file:

vmd/1.9.1

Read Documentation

• http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

Download

• http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Download the source package -- vmd-1.9.1.tar.gz

tar xf vmd-1.9.1.src.tar.gz

This creates two directories:

vmd-1.9.1 plugins

The "plugins" must be compiled first, before the main VMD application.

Installation Location

Decide on an installation location. A good one would be:

/mnt/HA/groups/myrsrchGrp/opt/vmd/1.9.1

Set an environment variable for convenience:

[juser@proteusa01 ~]$ export PREFIX=/mnt/HA/groups/myrsrcfGrp/opt/vmd/1.9.1

So, set an environment variable:

[juser@proteusa01 ~]$ export PLUGINDIR=${PREFIX}/plugins

And create the directory if not already there:

[juser@proteusa01 ~]$ mkdir -p $PLUGINDIR

Remember the two directories created by expanding the tarfile? Go to the one named vmd-1.9.1 to set another environment variable for convenience:

[juser@proteusa01 ~]$ cd vmd-1.9.1 [juser@proteusa01 vmd-1.9.1]$ [juser@proteusa01 vmd-1.9.1]$ export SRCDIR=$(pwd)

Build Plugins

Documentation: http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

Prerequisite: NetCDF

[juser@proteusi01 ~]$ module load netcdf/gcc [juser@proteusi01 ~]$ cd plugins

Set an environment variable:

[juser@proteusi01 ~]$ export NETCDFINC="-I${NETCDFINCLUDE}"

Unset an environment variable:

[juser@proteusi01 ~]$ unset NETCDFLIB

Edit the file "Make-arch" -- line 369:

"NETCDFLDFLAGS = -L${NETCDFDIR} -lnetcdf " \

Build:

[juser@proteusi01 plugins]$ make LINUXAMD64 >& Make.linuxamd64.out &

Install -- N.B. This requires the PLUGINDIR environment variable to be set properly. (See above.)

[juser@proteusi01 plugins]$ make distrib >& Make.distrib.out &

Build VMD

[juser@proteusi01 plugins]$ cd ../vmd-1.9.1

Set environment variables:

[juser@proteusa01 vmd-1.9.1]$ export VMDINSTALLBINDIR=${PREFIX}/bin [juser@proteusa01 vmd-1.9.1]$ export VMDINSTALLLIBRARYDIR=${PREFIX}/lib

Link the plugins directory:

[juser@proteusa01 vmd-1.9.1]$ ln -s $PLUGINDIR .

Configure:

[juser@proteusi01 vmd-1.9.1]$ ./configure LINUXAMD64 MESA FLTK TK IMD SILENT TCL PTHREADS ACTC LIBTACHYON NETCDF [juser@proteusi01 vmd-1.9.1]$ cd src

ACTC (Mesh Triangulation)

Download ACTC:

http://plunk.org/~grantham/public/actc/

Put it in proper place:

[juser@proteusa01 ~]$ mv actc-1.1.tar.gz ${SRCDIR}/lib

Expand:

[juser@proteusa01 ~]$ cd $SRCDIR/lib ; tar xf actc-1.1

Edit Makefile:

[juser@proteusa01 lib]$ cd actc-1.1

### Add this CC=gcc ### Modify this LIBDEST =      $(SRCDIR)/lib/actc/lib_LINUXAMD64 INCDEST =      $(SRCDIR)/lib/actc/include ### And modify this CFLAGS=-O3 -march=corei7-avx -mfpmath=sse

### And modify this (line 54): cp tc.h $(INCDEST)

Build:

[juser@proteusa01 actc-1.1]$ make

Install:

[juser@proteusa01 actc-1.1]$ make install

Fixes

Edit the Makefile:

### line 5 -- comment it out #.SILENT: ### line 17 GNUCOMPRESS=gzip ### line 443: ### replace "-I../lib/netcdf/include" with "-I$(NETCDFINCLUDE)" ### line 445: ### replace "-lMesaGL" by "-lGL", and "-lMesaGLU" by "-lGLU" LIBS        = -lGL -lGLU ... ### line 447: ### replace "-L../lib/netcdf/lib_LINUXAMD64" with "-L$(NETCDFDIR)"

Edit the file LibTachyonDisplayDevice.h. Change one line (#28):

#include <tachyon/tachyon.h>          // main Tachyon library header

Edit the file DispCmds.C line 37:

#include "tc.h"

Compilation

Build:

[juser@proteusa01 src]$ make -j 12

This creates the executable named vmd_LINUXAMD64 in the directory $(SRCDIR)/LINUXAMD64/

Install

Copy tcl scripts to the right place.

[juser@proteusa01 vmd-1.9.1]$ cd $PREFIX [juser@proteusa01 1.9.1]$ mkdir scripts [juser@proteusa01 1.9.1]$ cd $SRCDIR/scripts [juser@proteusa01 scripts]$ cp -R vmd $PREFIX/scripts

Copy shaders to the right place:

[juser@proteusa01 scripts]$ cd .. [juser@proteusa01 vmd-1.9.1]$ cp -R shaders $PREFIX

Copy executable to the right place:

[juser@proteusa01 vmd-1.9.1]$ mkdir $PREFIX/bin [juser@proteusa01 vmd-1.9.1]$ cp LINUXAMD64/vmd_LINUXAMD64 $PREFIX/bin

Set your PATH:

[juser@proteusa01 vmd-1.9.1]$ export PATH=${PREFIX}/bin:${PATH}

References

[1] VMD website