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Viewing changes to tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT

  • Committer: Package Import Robot
  • Author(s): Anton Gladky
  • Date: 2015-04-29 23:44:49 UTC
  • mfrom: (5.1.3 experimental)
  • Revision ID: package-import@ubuntu.com-20150429234449-mbhy9utku6hp6oq8
Tags: 0~20150313.gitfa668e1-1
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
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# This directory demonstrates how to run a long simulation of 
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# the "frustrated" coarse-grained protein confined in a frustrated
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# coarse-grained chaperonin (R=6, h=0.475) as described in:
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# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
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# (http://www.pnas.org/content/101/36/13192)
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#
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# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 
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#       instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" 
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#       (at the end of "system.lt") with "CHAP_INTERIOR_H0"
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#
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# Because this process takes a long time (even with the help of the chaperone)
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# I save the data relatively infrequently.
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#
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# -------- REQUIREMENTS: ---------
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# 1) This example requires the "USER-MISC" package.  (Use "make yes-USER-MISC")
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#   http://lammps.sandia.gov/doc/Section_start.html#start_3
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# 2) It also may require additional features and bug fixes for LAMMPS.
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#   be sure to download and copy the "additional_lammps_code" from 
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#   http://moltemplate.org     (upper-left corner menu)
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# 3) Unpack it
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# 4) copy the .cpp and .h files to the src folding of your lammps installation.
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# 5) Compile LAMMPS.
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-------------
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Instructions on how to build LAMMPS input files and 
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run a short simulation are provided in other README files.
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step 1)
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README_setup.sh
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step2)
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README_run.sh