RCD & EM examples

  • Last update: 19 March 2019
  • File size: 21.61 MB
  • Version: 1.0
  • Downloaded: 109
  • Author: López-Blanco JR and Chacón P
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# 
# Ab-initio loop modeling using experimental EM-maps information.
#
# Tested with RCD version: v1.40
#
# Please, download the latest version from:
# http://chaconlab.org/modeling/rcd/rcd-download/item/rcd-linux64
#

#
# 1) RAW SAMPLING (to compare with EM-filtered)
#

# SEQUENTIAL RUN
rcd_mpi_gnu loopem.txt -r --bench -n 1000 -x dunbrack.bin -d 0.5 --linear -t 0.99 --rasp -e 0 -o seq

# PARALLEL RUN
time mpirun.openmpi -np 4 rcd_mpi_gnu loopem.txt -r --bench -n 1000 -x dunbrack.bin -d 0.5 --linear -t 0.99 --rasp -e 0 -o par


#
# 2) EM-FILTERED SAMPLING
#

# SEQUENTIAL RUN
rcd_mpi_gnu loopem.txt -r --bench -n 1000 -x dunbrack.bin -d 0.5 --linear -t 0.99 --rasp -e 0 --em 0 --loco_best 10 -o seqEM

# PARALLEL RUN
time mpirun.openmpi -np 4 rcd_mpi_gnu loopem.txt -r --bench -n 1000 -x dunbrack.bin -d 0.5 --linear -t 0.99 --rasp -e 0 --em 0 --loco_best 10 -o parEM

# *Typical parallel version run-times with EM-filtration range from 1 minute for 1000 loops sampling to 10 minutes for 10000.


-------
CONTACT
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Please, feel free to contact with us!
(Any suggestion or bug report is welcome)

Jose Ramon Lopez-Blanco (PhD)
jrlopez(at)iqfr.csic.es

Pablo Chacon (PhD.)
pablo(at)chaconlab.org


Structural Bioinformatics Group
IQFR-CSIC - Madrid (Spain)
(http://chaconlab.org)