As a highly optimized parallel MD tool, compiled Desmond is around 20-30% faster than the pre-compiled version which is distrubuted in Schrodinger software. here are some steps for how to compile Desmond from source code.
1. download source code from http://www.deshawresearch.com/resources_desmond.html
2. install boost although each Linux OS may already have boost, but Desmond required boost version> =4.15.0, it is better to compile it manually. The source code can be download from http://sourceforge.net/projects/boost/files/boost/ > tar xvf boost_1_45_0.tar.bz2 > ./bootstrap.sh add the following line at the end of tools/build/v2/user-config.jam using mpi; > ./bjam install --prefix=/soft/boost1.45
3. install openmpi it is highly recommend for openmpi1.4.3 > ./configure --prefix=/soft/openmpi > make > make install
4. configure installation file file for Desmond >cp share/user-conf.sample.py user-conf.py edit it as following:
--------user-conf.py-------- # Copyright D. E. Shaw Research, 2011. ''' This configuration works in DESRES. At a minimum, to get a single node version of Desmond you will have to give the location of the Boost include and library files. To build a multi-node MPI version, you will have to give the same path information for MPI. Similarly for Python.
Build Desmond with scons --user-config=share/user-conf.sample.py
'''
import sys import os
if EXTRA_C_FLAGS == None: EXTRA_C_FLAGS = '' if EXTRA_CC_FLAGS == None: EXTRA_CC_FLAGS = '' if EXTRA_LINK_FLAGS == None: EXTRA_LINK_FLAGS = '' if EXTRA_LIBS == None: EXTRA_LIBS = '' if EXTRA_INCLUDE_PATH == None: EXTRA_INCLUDE_PATH = '' if EXTRA_LIBRARY_PATH == None: EXTRA_LIBRARY_PATH = '' USE_BFD=False
if sys.platform == 'win32' : THREADS = 'BOOST'
# When building for Windows, you will need to set the # DESRES_TARGET_ARCH variable as one of 'x86_64' or 'x86'. if os.getenv('DESRES_TARGET_ARCH') == 'x86_64' : larch = 'x64' elif os.getenv('DESRES_TARGET_ARCH') == 'x86' : larch = 'x86' else: print >>sys.stderr, "DESRES_TARGET_ARCH fail" sys.exit(1)
# Python # DESRES installs Python and numpy in separate path locations; your installation # will likely install numpy somewhere in the Python path hierarchy python_prefix = '/usr/lib64/python2.7' numpy_prefix = "/usr/lib64/python2.7/site-packages"
test for short MD: >cd /soft/desmond3.0.3 >./bin/desmond --include ./share/samples/dhfr.cfg --cfg boot.file=./share/samples/dhfr.dms --cfg mdsim.plugin.eneseq.name=dhfr.eneseq
test for restore checkpoint ./bin/desmond --restore checkpt