new example, polyethylene with CG level 10->1 and OPLS/AA ff

Author: jkrajniak

examples/pe_10/MyJobScript.sh

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+#!/bin/bash -l
+#PBS -N R_0_100  
+#PBS -l mem=8gb
+#PBS -l walltime=20:00:00
+#PBS -o Output.job
+#PBS -j oe
+#PBS -l nodes=1:ppn=20
+module load espressopp/adress_new 
+module load bakery-github-dev
+
+cd $PBS_O_WORKDIR
+
+mpirun -np 18 start_backmapping.py @params 

examples/pe_10/README.md

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+Polyethylene: case 3
+===========================
+
+ - force field: OPLS/AA
+ - chain length: 100 segments
+ - number of chains: 75
+ - CG mapping: 10 segments into one CG bead
+

examples/pe_10/aa/MyJobScript.sh

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+#!/bin/bash -l
+#PBS -N PE_423_NVT_1
+#PBS -l walltime=24:00:00
+#PBS -o Output.job
+#PBS -j oe
+#PBS -l nodes=1:ppn=24
+#PBS -M jakub.krajniak@cs.kuleuven.be
+#PBS -A lp_polymer_goa_project
+
+
+module purge
+module load GROMACS/5.0.4-intel-2014a-hybrid
+module remove impi
+module load impi
+MDRUN="mdrun_mpi -v" 
+GROMPP="grompp_mpi"
+
+cd $PBS_O_WORKDIR
+
+# Set up OpenMPI environment
+n_proc=$(cat $PBS_NODEFILE | wc -l)
+n_node=$(cat $PBS_NODEFILE | uniq | wc -l)
+#mpdboot -f $PBS_NODEFILE -n $n_node -r ssh -v
+
+mpirun -np $n_proc $MDRUN 
+
+mpdallexit

examples/pe_10/aa/conf.gro

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+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor - specify a full path if necessary.
+include                  = 
+define                   = 
+
+; RUN CONTROL PARAMETERS
+integrator               = md
+; Start time and timestep in ps
+tinit                    = 0
+dt                       = 0.001
+nsteps                   = 10000000
+; For exact run continuation or redoing part of a run
+init_step                = 0
+; mode for center of mass motion removal
+comm-mode                = Linear
+; number of steps for center of mass motion removal
+nstcomm                  = 10
+; group(s) for center of mass motion removal
+comm_grps                = System
+
+
+;periodic-molecules = yes
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+ld-seed                  = 1993
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+; Output frequency for energies to log file and energy file
+nstlog                   = 1000
+nstenergy                = 1000
+; Output frequency and precision for xtc file
+nstxtcout                = 5000
+xtc-precision            = 1000
+; This selects the subset of atoms for the xtc file. You can
+; select multiple groups. By default all atoms will be written.
+xtc_grps                 = System ;Protein 
+; Selection of energy groups
+energygrps               = System
+
+; NEIGHBORSEARCHING PARAMETERS
+; nblist update frequency
+cutoff-scheme            = verlet
+nstlist                  = 10
+; ns algorithm (simple or grid)
+ns_type                  = grid
+; Periodic boundary conditions: xyz (default), no (vacuum)
+; or full (infinite systems only)
+pbc                      = xyz
+; nblist cut-off        
+rlist                    = 1.2
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype              = cut-off
+rcoulomb-switch          = 0
+rcoulomb                 = 1.2
+; Relative dielectric constant for the medium and the reaction field
+epsilon_r                = 1
+epsilon_rf               = 1
+; Method for doing Van der Waals
+vdwtype                  = cut-off
+; cut-off lengths       
+rvdw-switch              = 0
+rvdw                     = 1.2
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr                 = No 
+; Extension of the potential lookup tables beyond the cut-off
+table-extension          = 1.0
+; Seperate tables between energy group pairs
+;energygrp_table          = A A   
+; Spacing for the PME/PPPM FFT grid
+fourierspacing           = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier_nx               = 0
+fourier_ny               = 0
+fourier_nz               = 0
+; EWALD/PME/PPPM parameters
+pme_order                = 4
+ewald_rtol               = 1e-05
+ewald_geometry           = 3d
+epsilon_surface          = 0
+optimize_fft             = no
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling  
+tcoupl                   = V-rescale; No ;Nose-Hoover 
+; Groups to couple separately
+tc-grps                  = System 
+; Time constant (ps) and reference temperature (K)
+tau_t                    = 1.0
+ref_t                    = 423
+; Pressure coupling     
+Pcoupl                   = No ;Parrinello-Rahman 
+pcoupltype               = isotropic
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau_p                    = 0.5
+compressibility          = 4.5e-5
+ref_p                    = 1.0
+; Random seed for Andersen thermostat
+andersen_seed            = 815131
+
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen_vel                  = yes
+gen_temp                 = 423
+gen_seed                 = -1
+
+; OPTIONS FOR BONDS    
+constraints              = none
+; Type of constraint algorithm
+constraint_algorithm     = LINCS
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR                = no
+; Relative tolerance of shake
+shake-tol                = 1e-04
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order              = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs_iter               = 2
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle          = 30
+; Convert harmonic bonds to morse potentials
+morse                    = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp_excl           = 
+