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namd-3_0-IMDv3.diff
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diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..3db89aa
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+# Project-level ignore patterns
+
+# Ignore dependencies
+fftw*
+tcl*
+
+# Ignore build artifacts
+Linux-x86_64*
diff --git a/IMDv3-dev.md b/IMDv3-dev.md
new file mode 100644
index 0000000..50f39b6
--- /dev/null
+++ b/IMDv3-dev.md
@@ -0,0 +1,160 @@
+# IMD v3 developement
+
+The IMDv3-dev branch focuses on the developement of a new IMD protocol for sending additional information via IMD.
+Details of the protocol can be found [here](https://github.com/Becksteinlab/imdclient/blob/protocolv3/docs/source/protocol_v3.rst).
+
+## Instructions for compiling and building NAMD
+
+### Dependencies and requirements
+
+Building a complete NAMD binary from source code requires:
+
+- working C and C++ compilers;
+- a compiled version of the Charm++/Converse library;
+- a compiled version of the TCL library and its header files;
+- a compiled version of the FFTW library and its header files;
+- a C shell (csh/tcsh) to run the script used to configure the build.
+
+NAMD can be compiled without TCL or FFTW, but certain features will be
+disabled. Fortunately, precompiled TCL and FFTW libraries are available from
+http://www.ks.uiuc.edu/Research/namd/libraries/. You may disable
+these options by specifying --without-tcl --without-fftw as options
+when you run the config script. Some files in arch may need editing
+to set the path to TCL and FFTW libraries correctly.
+
+### Building and Compiling Charm++
+
+As an example, here is the build sequence for 64-bit Linux workstations:
+
+Unpack NAMD and matching Charm++ source code:
+
+```
+ git clone https://github.com/amruthesht/namd-3.0.git
+ cd namd-3.0
+ tar xf charm-8.0.0.tar
+```
+
+Build and test the Charm++/Converse library (testing is optional)
+
+When using single-node multicore version:
+```
+ cd charm-8.0.0
+ ./build charm++ multicore-linux-x86_64 --with-production
+ cd multicore-linux-x86_64/tests/charm++/megatest
+ make
+ ./megatest +p4 (multicore does not support multiple nodes)
+ cd ../../../../..
+```
+
+When using InfiniBand UCX OpenMPI PMIx version:
+(Make sure modules and corresponding headers for openmpi and pmix are available and accessible before running this)
+```
+ cd charm-8.0.0
+ ./build charm++ ucx-linux-x86_64 ompipmix --with-production
+ cd ucx-linux-x86_64-ompipmix/tests/charm++/megatest
+ make
+ mpiexec -n 4 ./megatest
+ cd ../../../../..
+```
+
+When using MPI version:
+```
+ cd charm-8.0.0
+ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
+ cd mpi-linux-x86_64/tests/charm++/megatest
+ make pgm
+ mpiexec -n 4 ./megatest (run as any other MPI program on your cluster)
+ cd ../../../../..
+```
+
+The `mpiexec` command is run as any other OpenMPI or MPI program on your cluster on an intercative node. Make sure to request appropriate resources for it.
+
+### Installing header-only dependencies
+
+Download and install TCL and FFTW libraries:
+ (cd to `namd-3.0` if you're not already there)
+```
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
+ tar xzf fftw-linux-x86_64.tar.gz
+ mv linux-x86_64 fftw
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64.tar.gz
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64-threaded.tar.gz
+ tar xzf tcl8.6.13-linux-x86_64.tar.gz
+ tar xzf tcl8.6.13-linux-x86_64-threaded.tar.gz
+ mv tcl8.6.13-linux-x86_64 tcl
+ mv tcl8.6.13-linux-x86_64-threaded tcl-threaded
+```
+
+### Compiling and Building NAMD
+
+Set up build directory and compile for NAMD:
+multicore version:
+```
+ ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64
+```
+InfiniBand UCX version:
+```
+ ./config Linux-x86_64-g++ --charm-arch ucx-linux-x86_64-ompipmix
+```
+MPI version:
+```
+ ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
+```
+GPU-resident CUDA multicore version:
+```
+ ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64 --with-single-node-cuda
+```
+GPU-resident CUDA ethernet version:
+```
+ ./config Linux-x86_64-g++ --charm-arch netlrts-linux-x86_64 --with-single-node-cuda
+```
+GPU-resident HIP multicore version:
+```
+ ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64 --with-single-node-hip
+```
+GPU-resident HIP ethernet version:
+```
+ ./config Linux-x86_64-g++ --charm-arch netlrts-linux-x86_64 --with-single-node-hip
+```
+
+You might also need `--cuda-prefix CUDA_DIRECTORY` for the GPU ones, if needed.
+
+Finally, `make` the namd source files to create an executable
+
+```
+ cd Linux-x86_64-g++
+ make
+```
+
+## Input configuration options
+
+We have introduced new configuration settings in the input file `*.conf` in accordance with the protocol defined [here](https://github.com/Becksteinlab/imdclient/blob/protocolv3/docs/source/protocol_v3.rst). The following options and settings can be set in accordance with the user's need to stream data and trajectory information.
+
+#### General IMD options (same as v2)
+1. `IMDon` - streaming on or off (yes/no)
+2. `IMDport` - port number to listen on (typically 8888)
+3. `IMDfreq` - frequency to send data
+4. `IMDwait` - wait for client to connect before starting simulation (on/off)
+
+#### New IMD options (new in v3)
+5. `IMDversion` - 2 for VMD and 3 for latest protocol
+#### IMD session info settings (yes/no)
+6. `IMDsendPositions` - sending positions of entire system
+7. `IMDsendEnergies` - sending energies and bonded, non-bonded and other contributions
+8. `IMDsendTime` - sending time information (time, dt, step)
+9. `IMDsendBoxDimensions` - sending box dimensions (lattice vectors a, b, c). If box dimensions are not defined, default unit box is sent
+10. `IMDsendVelocities` - sending velocities of entire system
+11. `IMDsendForces` - sending forces on all atoms
+12. `IMDwrapPositions` - wrapping positions to box; applicable when IMDsendPositions is yes
+
+## Example Run
+
+Run an example simulation (this is a 66-atom simulation) and compare to the `-sample` output files (for seed 12345) in the dierctory:
+```
+ ./namd3 ../examples/alanin/shorter-run/alanin.conf
+```
+
+If running on a cluster with $N$ cores allocated for the job, one might have to run something like
+```
+ mpiexec -n N ./namd3 ../examples/alanin/shorter-run/alanin.conf
+```
\ No newline at end of file
diff --git a/examples/alanin/longer-run/alanin.conf b/examples/alanin/longer-run/alanin.conf
new file mode 100644
index 0000000..1a8e128
--- /dev/null
+++ b/examples/alanin/longer-run/alanin.conf
@@ -0,0 +1,28 @@
+# This is a test namd configuration file
+
+timestep 1.0
+numsteps 100000
+structure alanin.psf
+parameters alanin.params
+coordinates alanin.pdb
+exclude scaled1-4
+1-4scaling 0.4
+outputname output
+margin 1.0
+stepspercycle 20
+temperature 300
+
+langevin on
+langevinDamping 5
+langevinHydrogen no
+langevinTemp 300
+
+switching on
+switchdist 7.0
+cutoff 8.0
+pairlistdist 9.0
+
+IMDon yes
+IMDport 2030
+IMDfreq 1
+IMDwait on
diff --git a/examples/alanin/longer-run/alanin.params b/examples/alanin/longer-run/alanin.params
new file mode 100644
index 0000000..1690deb
--- /dev/null
+++ b/examples/alanin/longer-run/alanin.params
@@ -0,0 +1,402 @@
+remark - parameter file PARAM19 -
+remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
+remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
+remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
+
+set echo=false end
+!! - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974)
+!! - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
+!! - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1
+!! The default h-bond exponents are now 6-repul 4-attr
+!! ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++
+!! Switched from Slater-Kirkwood to simple mixing rules - AB
+!! Hbond parameters based on comparisons of dimer results with
+!! ab initio calculations. - WER 12/19/84
+!! Grouping of atom types for VDW parameters - BRB 1/3/85
+
+
+bond C C 450.0 1.38! B. R. GELIN THESIS AMIDE AND DIPEPTIDES
+bond C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT
+bond C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED
+bond C CH3E 405.0 1.52
+bond C CR1E 450.0 1.38
+bond C CT 405.0 1.53
+bond C N 471.0 1.33
+bond C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE
+bond C NH1 471.0 1.33
+bond C NH2 471.0 1.33
+bond C NP 471.0 1.33
+bond C NR 471.0 1.33
+bond C O 580.0 1.23
+bond C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O
+bond C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
+bond C OS 292.0 1.43! FROM DEP NORMAL MODE FIT
+bond CH1E CH1E 225.0 1.53
+bond CH1E CH2E 225.0 1.52
+bond CH1E CH3E 225.0 1.52
+bond CH1E N 422.0 1.45
+bond CH1E NH1 422.0 1.45
+bond CH1E NH2 422.0 1.45
+bond CH1E NH3 422.0 1.45
+bond CH1E OH1 400.0 1.42! FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
+bond CH2E CH2E 225.0 1.52
+bond CH2E CH3E 225.0 1.54
+bond CH2E CR1E 250.0 1.45! FROM WARSHEL AND KARPLUS 1972 JACS 96:5612
+bond CH2E N 422.0 1.45
+bond CH2E NH1 422.0 1.45
+bond CH2E NH2 422.0 1.45
+bond CH2E NH3 422.0 1.45
+bond CH2E OH1 400.0 1.42
+bond CH2E S 450.0 1.81! FROM PARMFIX9
+bond CH2E SH1E 450.0 1.81
+bond CH3E NH1 422.0 1.49
+bond CH3E NR 422.0 1.49 ! FOR NETROPSIN
+bond CH3E S 450.0 1.77! FROM PARMFIX9
+bond CH3E OS 292.0 1.38! FROM DEP NORMAL MODE FIT
+bond CM OM 1115.0 1.128! FROM CAUGHEY ET AL(1978),CARBON MONOXIDE
+bond CR1E CR1E 450.0 1.38
+bond CR1E NH1 450.0 1.305
+bond CR1E NR 450.0 1.305
+bond CT CT 200.0 1.53
+bond CT N 422.0 1.45
+bond CT NC2 422.0 1.45
+bond CT NH1 422.0 1.45
+bond CT NH2 422.0 1.45
+bond CT NH3 422.0 1.45
+bond CT OH1 400.0 1.42
+bond CT S 450.0 1.81
+!bond FE CM 258.0 1.79! FROM KROEKER ET AL(JCP:72:4846)
+!bond FE NP 500.0 2.09
+!bond FE NR 65.0 1.98! FROM NAGAI ET AL(1980)
+!bond FE OM 250.0 1.8! JUST A GUESS.
+bond H NH1 405.0 0.98! GELIN AND IR STRETCH 3200 CM 1
+bond H NH2 405.0 0.98
+bond H OH1 450.0 0.96! FROM IR STRETCH 3400 CM 1
+bond HA C 350.0 1.08
+bond HA CT 300.0 1.08
+bond HC NC2 405.0 1.00
+bond HC NH1 405.0 0.98
+bond HC NH3 405.0 1.04
+bond OC S 400.0 1.43
+bond OM OM 600.0 1.23! STRETCHING CONSTANT JUST A GUESS.
+bond S S 500.0 2.02
+
+
+angle C C C 70.0 106.5! FROM B. R. GELIN THESIS WITH HARMONIC
+angle C C CH2E 65.0 126.5! PART OF F TERMS INCORPORATED. ATOMS
+angle C C CH3E 65.0 126.5! WITH EXTENDED H COMPENSATED FOR LACK
+angle C C CR1E 70.0 122.5! OF H ANGLES.
+angle C C CT 70.0 126.5
+angle C C HA 40.0 120.0! AMIDE PARAMETERS FIT BY LEAST SQUARES
+angle C C NH1 65.0 109.0! TO N-METHYL ACETAMIDE VIBRATIONS.
+angle C C NP 65.0 112.5! MINIMIZATION OF N-METHYL ACETAMIDE.
+angle C C NR 65.0 112.5
+angle C C OH1 65.0 119.0
+angle C C O 65.0 119.0 ! FOR NETROPSIN
+angle CH1E C N 20.0 117.5
+angle CH1E C NH1 20.0 117.5
+angle CH1E C O 85.0 121.5
+angle CH1E C OC 85.0 117.5
+angle CH1E C OH1 85.0 120.0
+angle CH2E C CR1E 70.0 121.5
+angle CH2E C N 20.0 117.5
+angle CH2E C NH1 20.0 117.5
+angle CH2E C NH2 20.0 117.5
+angle CH2E C NC2 20.0 117.5 ! FOR NETROPSIN
+angle CH2E C NR 60.0 116.0
+angle CH2E C O 85.0 121.6
+angle CH2E C OC 85.0 118.5
+angle CH2E C OH1 85.0 120.0
+angle CH3E C N 20.0 117.5
+angle CH3E C NH1 20.0 117.5
+angle CH3E C O 85.0 121.5
+angle CR1E C CR1E 65.0 120.5
+angle CR1E C NH1 65.0 110.5! USED ONLY IN HIS, NOT IT TRP
+angle CR1E C NP 65.0 122.5
+angle CR1E C NR 65.0 122.5
+angle CR1E C OH1 65.0 119.0
+angle CT C N 20.0 117.5
+angle CT C NH1 20.0 117.5
+angle CT C NH2 20.0 117.5
+angle CT C O 85.0 121.5
+angle CT C OC 85.0 118.5
+angle CT C OH1 85.0 120.0
+angle HA C NH1 40.0 120.0
+angle HA C NH2 40.0 120.0
+angle HA C NR 40.0 120.0
+angle HA C O 85.0 121.5
+angle N C O 85.0 121.0
+angle NC2 C NC2 70.0 120.0
+angle NC2 C NH1 70.0 120.0
+angle NH1 C NR 70.0 120.0
+angle NH1 C O 65.0 121.0
+angle NH2 C O 65.0 121.0
+angle O C OH1 85.0 120.0
+angle OC C OC 85.0 122.5
+angle OS C CH1E 70.0 125.3! FROM PARDNA10
+angle OS C CH2E 70.0 125.3! - " -
+angle OS C O 70.0 120.0! - " -
+angle C CH1E CH1E 70.0 110.0
+angle C CH1E CH2E 70.0 109.5
+angle C CH1E CH3E 70.0 106.5
+angle C CH1E N 45.0 111.6
+angle C CH1E NH1 45.0 111.6
+angle C CH1E NH2 45.0 111.6
+angle C CH1E NH3 45.0 111.6
+angle CH1E CH1E CH2E 45.0 112.5
+angle CH1E CH1E CH3E 45.0 111.0
+angle CH1E CH1E NH1 50.0 110.0
+angle CH1E CH1E NH2 50.0 109.5
+angle CH1E CH1E NH3 50.0 107.5
+angle CH1E CH1E OH1 50.0 104.5
+angle CH2E CH1E CH3E 50.0 111.5
+angle CH2E CH1E N 65.0 104.0
+angle CH2E CH1E NH1 65.0 110.0
+angle CH2E CH1E NH2 65.0 110.0
+angle CH2E CH1E NH3 65.0 110.0
+angle CH3E CH1E CH3E 50.0 111.0
+angle CH3E CH1E NH1 65.0 108.5
+angle CH3E CH1E NH2 65.0 109.5
+angle CH3E CH1E NH3 65.0 109.5
+angle CH3E CH1E OH1 60.0 110.5
+angle C CH2E CH1E 70.0 112.5
+angle C CH2E CH2E 70.0 113.0
+angle C CH2E NH1 70.0 111.6
+angle C CH2E NH2 70.0 111.6
+angle C CH2E NH3 70.0 111.6
+angle CH1E CH2E CH1E 45.0 117.0
+angle CH1E CH2E CH2E 45.0 112.5
+angle CH1E CH2E CH3E 45.0 113.0
+angle CH1E CH2E OH1 45.0 111.0
+angle CH3E CH2E OH1 45.0 111.0
+angle CH1E CH2E S 50.0 112.5
+angle CH1E CH2E SH1E 50.0 112.5
+angle CH2E CH2E CH2E 45.0 110.0
+angle CH2E CH2E CH3E 45.0 111.0
+angle CH2E CH2E N 65.0 105.0
+angle CH2E CH2E NH1 65.0 111.0
+angle CH2E CH2E NH2 65.0 109.5
+angle CH2E CH2E NH3 65.0 110.5
+angle CH2E CH2E S 50.0 112.5
+angle C CR1E C 90.0 126.5
+angle C CR1E CH2E 90.0 122.0
+angle C CR1E CR1E 90.0 119.0
+angle C CR1E NH1 90.0 109.5
+angle C CR1E NR 90.0 106.5
+angle CR1E CR1E CR1E 90.0 120.5
+angle NH1 CR1E NH1 70.0 109.0
+angle NH1 CR1E NR 70.0 109.0
+angle C CT CT 70.0 109.5
+angle C CT HA 70.0 109.5
+angle C CT N 70.0 111.6
+angle C CT NH1 70.0 111.6
+angle C CT NH2 70.0 111.6
+angle C CT NH3 70.0 111.6
+angle CT CT CT 45.0 111.00
+angle CT CT HA 40.0 109.50
+angle CT CT N 65.0 105.00
+angle CT CT NC2 65.0 110.00
+angle CT CT NH1 65.0 110.00
+angle CT CT NH2 65.0 110.00
+angle CT CT NH3 65.0 110.00
+angle CT CT OH1 50.0 109.50
+angle CT CT S 50.0 112.50
+angle HA CT HA 40.0 109.5
+angle HA CT N 50.0 109.5
+angle HA CT NC2 50.0 109.5
+angle HA CT NH1 50.0 109.5
+angle HA CT NH3 50.0 109.5
+angle HA CT OH1 50.0 109.5
+angle HA CT S 40.0 109.5
+!angle FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980)
+angle C N CH1E 80.0 120.0
+angle C N CH2E 80.0 120.0
+angle C N CT 80.0 120.0
+angle CH1E N CH2E 60.0 110.0
+angle CH1E N CH3E 60.0 110.0
+angle CH2E N CH3E 60.0 109.5
+angle CT N CT 60.0 110.0
+angle C NC2 CT 80.0 120.0
+angle C NC2 HC 35.0 120.0
+angle CT NC2 HC 35.0 120.0
+angle HC NC2 HC 40.0 120.0
+angle C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG)
+angle C NH1 CH1E 77.5 120.0
+angle C NH1 CH2E 77.5 120.0
+angle C NH1 CH3E 77.5 120.0
+angle C NH1 CR1E 60.0 108.0
+angle C NH1 CT 80.0 120.0
+angle C NH1 H 30.0 120.0
+angle CH1E NH1 CH3E 60.0 120.0
+angle CH1E NH1 H 35.0 120.0
+angle CH2E NH1 CH3E 60.0 120.0
+angle CH2E NH1 H 35.0 120.0
+angle CH3E NH1 H 35.0 120.0
+angle CR1E NH1 CR1E 65.0 110.0
+angle CR1E NH1 H 35.0 120.0
+angle CT NH1 H 35.0 120.0
+angle C NH2 H 30.0 120.0
+angle CH1E NH2 CH2E 60.0 120.0
+angle CH1E NH2 H 35.0 120.0
+angle CH2E NH2 H 35.0 120.0
+angle CT NH2 H 35.0 120.0
+angle H NH2 H 40.0 125.0
+angle C NP C 70.0 102.5
+!angle C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9
+angle C NR C 70.0 102.5
+angle C NR CR1E 70.0 109.5
+angle CH3E NR CR1E 70.0 109.5 ! FOR NETROPSIN
+angle CH3E NR C 70.0 109.5 ! FOR NETROPSIN
+angle CR1E NR CR1E 65.0 110.0
+!angle CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9
+angle CH1E NH3 HC 35.0 109.5
+angle CH1E NH3 CH2E 35.0 109.5
+angle CH2E NH3 HC 35.0 109.5
+angle CT NH3 HC 35.0 109.5
+angle HC NH3 HC 40.0 109.5
+angle C OH1 H 50.0 109.5
+angle CH1E OH1 H 35.0 109.5
+angle CH2E OH1 H 35.0 109.5
+angle CT OH1 H 35.0 109.5
+!angle FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS.
+angle C OS CH3E 46.5 120.5! FROM PARDNA10
+angle CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IR
+angle CH2E S S 50.0 104.2
+angle CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9
+angle CT S S 50.0 104.2
+angle OC S OC 85.0 109.5! FORCE CONSTANT JST A GUESS.
+!angle NP FE CM 5.0 90.0
+!angle NP FE NP 50.0 90.0
+!angle NP FE NR 5.0 115.0
+!angle NP FE OM 5.0 90.0! JUST A GUESS FROM EXISTING FE CM DATA
+!angle NR FE CM 5.0 180.0
+!angle NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA
+
+
+dihe CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL.
+dihe CH2E C N CH1E 10.0 2 180.0
+dihe CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1
+dihe CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81
+dihe CR1E C C NH1 2.5 2 180.0
+dihe X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDES
+dihe X C CH2E X 0.0 3 0.0! USING A SINGLE
+dihe X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHER
+dihe X C CT X 0.0 3 0.0! THAN MULTIPLE TORSIONS.
+dihe X C N X 8.2 2 180.0! ALKANE TORSION REDUCED TO
+dihe X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITH
+dihe X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER.
+dihe X C NH2 X 8.2 2 180.0
+dihe X C OH1 X 1.8 2 180.0
+dihe X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1
+dihe X CH1E CH1E X 1.6 3 0.0
+dihe X CH1E CH2E X 1.6 3 0.0
+dihe X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OF
+dihe X CH1E NH1 X 0.3 3 0.0! EXP. DATA AND 6 31G CALC.
+dihe X CH1E NH2 X 1.8 3 0.0! PROTONATED SECONDARY AMINE
+dihe X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BOND
+dihe X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOH
+dihe X CH2E CH2E X 1.6 3 0.0
+dihe X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTS
+dihe X CH2E NH1 X 0.3 3 0.0
+dihe X CH2E NH2 X 0.6 3 0.0
+dihe X CH2E NH3 X 0.6 3 0.0
+dihe X CH2E OH1 X 0.5 3 0.0
+dihe X CH2E S X 1.2 2 0.0
+dihe X CT CT X 1.6 3 0.0
+dihe X CT N X 0.3 3 0.0! SEE CH1E COMMENTS
+dihe X CT NC2 X 0.3 3 0.0
+dihe X CT NH1 X 0.3 3 0.0
+dihe X CT NH2 X 0.6 3 0.0
+dihe X CT NH3 X 0.6 3 0.0
+dihe X CT OH1 X 0.5 3 0.0
+dihe X CT S X 1.2 2 0.0
+!dihe X FE NR X 0.05 4 0.0
+!dihe X FE CM X 0.05 4 0.0
+!dihe X FE OM X 0.00 4 0.0
+dihe X S S X 4.0 2 0.0! FROM EXP.R BARRI
+
+
+impr C C CR1E CH2E 90.0 0 0.0!GIVE 220 CM 1 METHYL OOP FOR TOLUENE.
+impr C CR1E C CH2E 90.0 0 0.0!USED HERE FOR TRP CG OUT OF PLANE
+impr C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOP
+impr C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOP
+impr C NH1 CR1E CH2E 90.0 0 0.0!
+impr C CR1E CR1E OH1 150.0 0 0.0! GIVE 249 CM 1 PHENOL OH OOP.
+impr C H H NH2 45.0 0 0.0! PRIMARY AMIDES (ASN AND GLN) OOP
+impr C OC OC CH1E 100.0 0 0.0! CARBOXYL OUT OF PLANE.
+impr C OC OC CH2E 100.0 0 0.0!
+impr C X X C 25.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS
+impr C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1
+impr C X X CH3E 90.0 0 0.0
+impr C X X CR1E 25.0 0 0.0
+impr C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS
+impr C X X HA 75.0 0 0.0!
+impr C X X NH1 100.0 0 0.0! AMIDES FIT TO N METHYL ACETAMIDE.
+impr C X X O 100.0 0 0.0
+impr C X X OC 100.0 0 0.0
+impr C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOP
+impr CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3
+impr CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40
+impr CH1E X X CH3E 55.0 0 35.26439
+impr CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENE
+impr CR1E X X NH1 25.0 0 0.0! SAME AS ABOVE FOR LACK OF VALUES
+!impr FE X X NP 20.0 0 0.0! FROM PARMFIX9
+impr H X X O 45.0 0 0.0
+impr N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENS
+impr N X X CH2E 45.0 0 0.0
+impr N X X CT 45.0 0 0.0
+impr NC2 X X CT 45.0 0 0.0
+impr NC2 X X HC 45.0 0 0.0
+impr NH1 X X CH1E 45.0 0 0.0
+impr NH1 X X CH2E 45.0 0 0.0
+impr NH1 X X CH3E 45.0 0 0.0
+impr NH1 X X CT 45.0 0 0.0
+impr NH1 X X H 45.0 0 0.0! AMIDES PROTON OOP
+impr NH1 X X NH1 25.0 0 0.0!
+impr NH1 X X NR 25.0 0 0.0
+impr NH2 X X H 45.0 0 0.0
+impr NR X X C 25.0 0 0.0
+impr NR X X CR1E 25.0 0 0.0
+impr NR X X CT 25.0 0 0.0
+impr NR X X CH3E 25.0 0 0.0 ! FOR NETROPSIN
+
+
+
+{* nonbonding parameter section *}
+{* ============================ *}
+
+ ! eps sigma eps(1:4) sigma(1:4)
+ ! (kcal/mol) (A)
+ ! ---------------------------------------
+ NONBonded H 0.0498 1.4254 0.0498 1.4254
+ NONBonded HA 0.0450 2.6157 0.0450 2.6157 !- charged group.
+ NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius
+ !
+ NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon
+ NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \
+ NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons
+ NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! /
+!! NONBonded CM 0.0262 4.4367 0.1000 3.3854
+ NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons
+!! NONBonded CT 0.0262 4.4367 0.1000 3.3854
+ !
+ NONBonded N 0.2384 2.8509 0.2384 2.8509
+ NONBonded NC2 0.2384 2.8509 0.2384 2.8509
+ NONBonded NH1 0.2384 2.8509 0.2384 2.8509
+ NONBonded NH2 0.2384 2.8509 0.2384 2.8509
+ NONBonded NH3 0.2384 2.8509 0.2384 2.8509
+ NONBonded NP 0.2384 2.8509 0.2384 2.8509
+ NONBonded NR 0.2384 2.8509 0.2384 2.8509
+ !
+ NONBonded O 0.1591 2.8509 0.1591 2.8509
+ NONBonded OC 0.6469 2.8509 0.6469 2.8509
+ NONBonded OH1 0.1591 2.8509 0.1591 2.8509
+!! NONBonded OM 0.1591 2.8509 0.1591 2.8509
+ NONBonded OS 0.1591 2.8509 0.1591 2.8509
+ !
+ NONBonded S 0.0430 3.3676 0.0430 3.3676
+ NONBonded SH1E 0.0430 3.3676 0.0430 3.3676
+ !
+!! NONBONDED FE 0.0000 1.1582 0.0000 1.1582
+
+set echo=true end
diff --git a/examples/alanin/longer-run/alanin.pdb b/examples/alanin/longer-run/alanin.pdb
new file mode 100644
index 0000000..8403a01
--- /dev/null
+++ b/examples/alanin/longer-run/alanin.pdb
@@ -0,0 +1,77 @@
+REMARK FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PDB"
+REMARK PARAM11.PRO ( from PARAM6A )
+REMARK ===========
+REMARK PROTEIN PARAMETERS:
+REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
+REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
+REMARK LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4
+REMARK CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.
+REMARK JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
+REMARK DATE:16-Feb-89 11:21:32 created by user: nonella
+ATOM 1 CA ACE 1 -2.184 0.591 0.910 1.00 7.00 MAIN
+ATOM 2 C ACE 1 -0.665 0.627 0.966 1.00 0.00 MAIN
+ATOM 3 O ACE 1 -0.069 1.213 1.868 1.00 0.00 MAIN
+ATOM 4 N ALA 2 0.000 0.000 0.000 1.00 3.00 MAIN
+ATOM 5 H ALA 2 -0.490 -0.462 -0.712 1.00 0.00 MAIN
+ATOM 6 CA ALA 2 1.450 0.000 0.000 1.00 7.00 MAIN
+ATOM 7 CB ALA 2 1.969 -0.670 -1.262 1.00 0.00 MAIN
+ATOM 8 C ALA 2 2.010 1.413 0.000 1.00 0.00 MAIN
+ATOM 9 O ALA 2 2.911 1.748 0.767 1.00 1.00 MAIN
+ATOM 10 N ALA 3 1.488 2.280 -0.863 1.00 0.00 MAIN
+ATOM 11 H ALA 3 0.770 1.998 -1.467 1.00 4.00 MAIN
+ATOM 12 CA ALA 3 1.981 3.643 -0.909 1.00 7.00 MAIN
+ATOM 13 CB ALA 3 1.147 4.464 -1.880 1.00 0.00 MAIN
+ATOM 14 C ALA 3 1.865 4.326 0.444 1.00 0.00 MAIN
+ATOM 15 O ALA 3 2.801 4.963 0.924 1.00 0.00 MAIN
+ATOM 16 N ALA 4 0.710 4.211 1.093 1.00 9.00 MAIN
+ATOM 17 H ALA 4 -0.026 3.700 0.697 1.00 0.00 MAIN
+ATOM 18 CA ALA 4 0.541 4.841 2.388 1.00 7.00 MAIN
+ATOM 19 CB ALA 4 -0.809 4.462 2.976 1.00 8.00 MAIN
+ATOM 20 C ALA 4 1.591 4.371 3.381 1.00 0.00 MAIN
+ATOM 21 O ALA 4 2.212 5.167 4.085 1.00 0.00 MAIN
+ATOM 22 N ALA 5 1.818 3.063 3.463 1.00 0.00 MAIN
+ATOM 23 H ALA 5 1.315 2.443 2.895 1.00 0.00 MAIN
+ATOM 24 CA ALA 5 2.809 2.556 4.392 1.00 7.00 MAIN
+ATOM 25 CB ALA 5 2.970 1.055 4.209 1.00 0.00 MAIN
+ATOM 26 C ALA 5 4.176 3.170 4.142 1.00 0.00 MAIN
+ATOM 27 O ALA 5 4.859 3.615 5.064 1.00 0.00 MAIN
+ATOM 28 N ALA 6 4.611 3.212 2.886 1.00 0.00 MAIN
+ATOM 29 H ALA 6 4.055 2.853 2.163 1.00 0.00 MAIN
+ATOM 30 CA ALA 6 5.908 3.786 2.586 1.00 7.00 MAIN
+ATOM 31 CB ALA 6 6.121 3.830 1.082 1.00 0.00 MAIN
+ATOM 32 C ALA 6 6.012 5.221 3.079 1.00 0.00 MAIN
+ATOM 33 O ALA 6 6.992 5.614 3.710 1.00 0.00 MAIN
+ATOM 34 N ALA 7 5.002 6.040 2.802 1.00 0.00 MAIN
+ATOM 35 H ALA 7 4.228 5.711 2.297 1.00 0.00 MAIN
+ATOM 36 CA ALA 7 5.044 7.419 3.245 1.00 7.00 MAIN
+ATOM 37 CB ALA 7 3.730 8.110 2.918 1.00 0.00 MAIN
+ATOM 38 C ALA 7 5.219 7.518 4.752 1.00 0.00 MAIN
+ATOM 39 O ALA 7 6.045 8.278 5.255 1.00 0.00 MAIN
+ATOM 40 N ALA 8 4.445 6.748 5.512 1.00 0.00 MAIN
+ATOM 41 H ALA 8 3.792 6.148 5.096 1.00 0.00 MAIN
+ATOM 42 CA ALA 8 4.566 6.799 6.956 1.00 7.00 MAIN
+ATOM 43 CB ALA 8 3.670 5.747 7.589 1.00 0.00 MAIN
+ATOM 44 C ALA 8 5.984 6.488 7.409 1.00 0.00 MAIN
+ATOM 45 O ALA 8 6.560 7.186 8.241 1.00 0.00 MAIN
+ATOM 46 N ALA 9 6.582 5.429 6.871 1.00 0.00 MAIN
+ATOM 47 H ALA 9 6.109 4.882 6.209 1.00 0.00 MAIN
+ATOM 48 CA ALA 9 7.934 5.082 7.264 1.00 7.00 MAIN
+ATOM 49 CB ALA 9 8.436 3.918 6.425 1.00 0.00 MAIN
+ATOM 50 C ALA 9 8.898 6.233 7.027 1.00 0.00 MAIN
+ATOM 51 O ALA 9 9.705 6.584 7.887 1.00 0.00 MAIN
+ATOM 52 N ALA 10 8.839 6.851 5.851 1.00 0.00 MAIN
+ATOM 53 H ALA 10 8.190 6.560 5.176 1.00 0.00 MAIN
+ATOM 54 CA ALA 10 9.733 7.956 5.567 1.00 7.00 MAIN
+ATOM 55 CB ALA 10 9.388 8.570 4.219 1.00 0.00 MAIN
+ATOM 56 C ALA 10 9.595 9.067 6.595 1.00 0.00 MAIN
+ATOM 57 O ALA 10 10.580 9.587 7.117 1.00 0.00 MAIN
+ATOM 58 N ALA 11 8.364 9.460 6.912 1.00 0.00 MAIN
+ATOM 59 H ALA 11 7.590 9.036 6.488 1.00 0.00 MAIN
+ATOM 60 CA ALA 11 8.169 10.516 7.887 1.00 7.00 MAIN
+ATOM 61 CB ALA 11 6.686 10.695 8.168 1.00 0.00 MAIN
+ATOM 62 C ALA 11 8.823 10.177 9.217 1.00 0.00 MAIN
+ATOM 63 O ALA 11 9.523 10.992 9.815 1.00 0.00 MAIN
+ATOM 64 N CBX 12 8.610 8.962 9.714 1.00 0.00 MAIN
+ATOM 65 H CBX 12 8.050 8.324 9.225 1.00 0.00 MAIN
+ATOM 66 CA CBX 12 9.223 8.571 11.014 1.00 0.00 MAIN
+END
diff --git a/examples/alanin/longer-run/alanin.psf b/examples/alanin/longer-run/alanin.psf
new file mode 100644
index 0000000..7587766
--- /dev/null
+++ b/examples/alanin/longer-run/alanin.psf
@@ -0,0 +1,206 @@
+PSF
+
+ 11 !NTITLE
+ REMARKS FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PSF"
+ REMARKS PARAM11.PRO ( from PARAM6A )
+ REMARKS ===========
+ REMARKS PROTEIN PARAMETERS:
+ REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
+ REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
+ REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4
+ REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.
+ REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
+ REMARKS
+ REMARKS DATE:16-Feb-89 11:21:29 created by user: nonella
+
+ 66 !NATOM
+ 1 MAIN 1 ACE CA CH3E 0.000000E+00 15.0350 0
+ 2 MAIN 1 ACE C C 0.450000 12.0110 0
+ 3 MAIN 1 ACE O O -0.450000 15.9994 0
+ 4 MAIN 2 ALA N NH1 -0.350000 14.0067 0
+ 5 MAIN 2 ALA H H 0.250000 1.00800 0
+ 6 MAIN 2 ALA CA CH1E 0.100000 13.0190 0
+ 7 MAIN 2 ALA CB CH3E 0.000000E+00 15.0350 0
+ 8 MAIN 2 ALA C C 0.450000 12.0110 0
+ 9 MAIN 2 ALA O O -0.450000 15.9994 0
+ 10 MAIN 3 ALA N NH1 -0.350000 14.0067 0
+ 11 MAIN 3 ALA H H 0.250000 1.00800 0
+ 12 MAIN 3 ALA CA CH1E 0.100000 13.0190 0
+ 13 MAIN 3 ALA CB CH3E 0.000000E+00 15.0350 0
+ 14 MAIN 3 ALA C C 0.450000 12.0110 0
+ 15 MAIN 3 ALA O O -0.450000 15.9994 0
+ 16 MAIN 4 ALA N NH1 -0.350000 14.0067 0
+ 17 MAIN 4 ALA H H 0.250000 1.00800 0
+ 18 MAIN 4 ALA CA CH1E 0.100000 13.0190 0
+ 19 MAIN 4 ALA CB CH3E 0.000000E+00 15.0350 0
+ 20 MAIN 4 ALA C C 0.450000 12.0110 0
+ 21 MAIN 4 ALA O O -0.450000 15.9994 0
+ 22 MAIN 5 ALA N NH1 -0.350000 14.0067 0
+ 23 MAIN 5 ALA H H 0.250000 1.00800 0
+ 24 MAIN 5 ALA CA CH1E 0.100000 13.0190 0
+ 25 MAIN 5 ALA CB CH3E 0.000000E+00 15.0350 0
+ 26 MAIN 5 ALA C C 0.450000 12.0110 0
+ 27 MAIN 5 ALA O O -0.450000 15.9994 0
+ 28 MAIN 6 ALA N NH1 -0.350000 14.0067 0
+ 29 MAIN 6 ALA H H 0.250000 1.00800 0
+ 30 MAIN 6 ALA CA CH1E 0.100000 13.0190 0
+ 31 MAIN 6 ALA CB CH3E 0.000000E+00 15.0350 0
+ 32 MAIN 6 ALA C C 0.450000 12.0110 0
+ 33 MAIN 6 ALA O O -0.450000 15.9994 0
+ 34 MAIN 7 ALA N NH1 -0.350000 14.0067 0
+ 35 MAIN 7 ALA H H 0.250000 1.00800 0
+ 36 MAIN 7 ALA CA CH1E 0.100000 13.0190 0
+ 37 MAIN 7 ALA CB CH3E 0.000000E+00 15.0350 0
+ 38 MAIN 7 ALA C C 0.450000 12.0110 0
+ 39 MAIN 7 ALA O O -0.450000 15.9994 0
+ 40 MAIN 8 ALA N NH1 -0.350000 14.0067 0
+ 41 MAIN 8 ALA H H 0.250000 1.00800 0
+ 42 MAIN 8 ALA CA CH1E 0.100000 13.0190 0
+ 43 MAIN 8 ALA CB CH3E 0.000000E+00 15.0350 0
+ 44 MAIN 8 ALA C C 0.450000 12.0110 0
+ 45 MAIN 8 ALA O O -0.450000 15.9994 0
+ 46 MAIN 9 ALA N NH1 -0.350000 14.0067 0
+ 47 MAIN 9 ALA H H 0.250000 1.00800 0
+ 48 MAIN 9 ALA CA CH1E 0.100000 13.0190 0
+ 49 MAIN 9 ALA CB CH3E 0.000000E+00 15.0350 0
+ 50 MAIN 9 ALA C C 0.450000 12.0110 0
+ 51 MAIN 9 ALA O O -0.450000 15.9994 0
+ 52 MAIN 10 ALA N NH1 -0.350000 14.0067 0
+ 53 MAIN 10 ALA H H 0.250000 1.00800 0
+ 54 MAIN 10 ALA CA CH1E 0.100000 13.0190 0
+ 55 MAIN 10 ALA CB CH3E 0.000000E+00 15.0350 0
+ 56 MAIN 10 ALA C C 0.450000 12.0110 0
+ 57 MAIN 10 ALA O O -0.450000 15.9994 0
+ 58 MAIN 11 ALA N NH1 -0.350000 14.0067 0
+ 59 MAIN 11 ALA H H 0.250000 1.00800 0
+ 60 MAIN 11 ALA CA CH1E 0.100000 13.0190 0
+ 61 MAIN 11 ALA CB CH3E 0.000000E+00 15.0350 0
+ 62 MAIN 11 ALA C C 0.450000 12.0110 0
+ 63 MAIN 11 ALA O O -0.450000 15.9994 0
+ 64 MAIN 12 CBX N NH1 -0.350000 14.0067 0
+ 65 MAIN 12 CBX H H 0.250000 1.00800 0
+ 66 MAIN 12 CBX CA CH3E 0.100000 15.0350 0
+
+ 65 !NBOND: bonds
+ 1 2 2 3 4 6 6 8
+ 8 9 4 5 6 7 2 4
+ 10 12 12 14 14 15 10 11
+ 12 13 8 10 16 18 18 20
+ 20 21 16 17 18 19 14 16
+ 22 24 24 26 26 27 22 23
+ 24 25 20 22 28 30 30 32
+ 32 33 28 29 30 31 26 28
+ 34 36 36 38 38 39 34 35
+ 36 37 32 34 40 42 42 44
+ 44 45 40 41 42 43 38 40
+ 46 48 48 50 50 51 46 47
+ 48 49 44 46 52 54 54 56
+ 56 57 52 53 54 55 50 52
+ 58 60 60 62 62 63 58 59
+ 60 61 56 58 64 66 64 65
+ 62 64
+
+ 96 !NTHETA: angles
+ 1 2 3 4 6 8 6 4 5
+ 4 6 7 6 8 9 8 6 7
+ 1 2 4 3 2 4 2 4 6
+ 2 4 5 10 12 14 12 10 11
+ 10 12 13 12 14 15 14 12 13
+ 6 8 10 9 8 10 8 10 12
+ 8 10 11 16 18 20 18 16 17
+ 16 18 19 18 20 21 20 18 19
+ 12 14 16 15 14 16 14 16 18
+ 14 16 17 22 24 26 24 22 23
+ 22 24 25 24 26 27 26 24 25
+ 18 20 22 21 20 22 20 22 24
+ 20 22 23 28 30 32 30 28 29
+ 28 30 31 30 32 33 32 30 31
+ 24 26 28 27 26 28 26 28 30
+ 26 28 29 34 36 38 36 34 35
+ 34 36 37 36 38 39 38 36 37
+ 30 32 34 33 32 34 32 34 36
+ 32 34 35 40 42 44 42 40 41
+ 40 42 43 42 44 45 44 42 43
+ 36 38 40 39 38 40 38 40 42
+ 38 40 41 46 48 50 48 46 47
+ 46 48 49 48 50 51 50 48 49
+ 42 44 46 45 44 46 44 46 48
+ 44 46 47 52 54 56 54 52 53
+ 52 54 55 54 56 57 56 54 55
+ 48 50 52 51 50 52 50 52 54
+ 50 52 53 58 60 62 60 58 59
+ 58 60 61 60 62 63 62 60 61
+ 54 56 58 57 56 58 56 58 60
+ 56 58 59 66 64 65 60 62 64
+ 63 62 64 62 64 66 62 64 65
+
+ 31 !NPHI: dihedrals
+ 2 4 6 8 1 2 4 6
+ 8 10 12 14 4 6 8 10
+ 6 8 10 12 14 16 18 20
+ 10 12 14 16 12 14 16 18
+ 20 22 24 26 16 18 20 22
+ 18 20 22 24 26 28 30 32
+ 22 24 26 28 24 26 28 30
+ 32 34 36 38 28 30 32 34
+ 30 32 34 36 38 40 42 44
+ 34 36 38 40 36 38 40 42
+ 44 46 48 50 40 42 44 46
+ 42 44 46 48 50 52 54 56
+ 46 48 50 52 48 50 52 54
+ 56 58 60 62 52 54 56 58
+ 54 56 58 60 58 60 62 64
+ 60 62 64 66
+
+ 32 !NIMPHI: impropers
+ 6 4 8 7 2 1 4 3
+ 4 2 6 5 12 10 14 13
+ 8 6 10 9 10 8 12 11
+ 18 16 20 19 14 12 16 15
+ 16 14 18 17 24 22 26 25
+ 20 18 22 21 22 20 24 23
+ 30 28 32 31 26 24 28 27
+ 28 26 30 29 36 34 38 37
+ 32 30 34 33 34 32 36 35
+ 42 40 44 43 38 36 40 39
+ 40 38 42 41 48 46 50 49
+ 44 42 46 45 46 44 48 47
+ 54 52 56 55 50 48 52 51
+ 52 50 54 53 60 58 62 61
+ 56 54 58 57 58 56 60 59
+ 62 60 64 63 64 62 66 65
+
+ 11 !NDON: donors
+ 4 5 10 11 16 17 22 23
+ 28 29 34 35 40 41 46 47
+ 52 53 58 59 64 65
+
+ 11 !NACC: acceptors
+ 3 2 9 8 15 14 21 20
+ 27 26 33 32 39 38 45 44
+ 51 50 57 56 63 62
+
+ 0 !NNB
+
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0
+
+ 33 0 !NGRP
+ 0 0 0 1 0 0 3 0 0
+ 6 0 0 7 0 0 9 0 0
+ 12 0 0 13 0 0 15 0 0
+ 18 0 0 19 0 0 21 0 0
+ 24 0 0 25 0 0 27 0 0
+ 30 0 0 31 0 0 33 0 0
+ 36 0 0 37 0 0 39 0 0
+ 42 0 0 43 0 0 45 0 0
+ 48 0 0 49 0 0 51 0 0
+ 54 0 0 55 0 0 57 0 0
+ 60 0 0 61 0 0 63 0 0
diff --git a/examples/alanin/shorter-run/alanin.conf b/examples/alanin/shorter-run/alanin.conf
new file mode 100644
index 0000000..876d453
--- /dev/null
+++ b/examples/alanin/shorter-run/alanin.conf
@@ -0,0 +1,73 @@
+# This is a test namd configuration file
+
+timestep 0.5
+numsteps 10
+structure alanin.psf
+parameters alanin.params
+coordinates alanin.pdb
+exclude scaled1-4
+1-4scaling 0.4
+outputname output[myReplica]
+margin 1.0
+stepspercycle 3
+temperature 0
+
+switching on
+switchdist 7.0
+cutoff 8.0
+pairlistdist 9.0
+
+dcdfile alanin.dcd
+dcdfreq 1
+# If Box dimensions are defined, the DCD file can contain the box dimensions via the following
+#DCDunitcell yes
+
+velDCDfile alanin.vel
+velDCDfreq 1
+
+forceDCDfile alanin.force
+forceDCDfreq 1
+
+#restartname alanin.restart
+#restartfreq 10
+
+#langevin on
+#langevinTemp 300.0
+#langevincol O
+
+#constraints on
+
+#fma on
+
+seed 12345
+
+# IMD parameters
+
+# standard IMD parameters
+# IMDon streaming -- on or off
+IMDon yes
+# IMDport -- port number to listen on
+IMDport 8888
+# IMDfreq -- frequency to send data
+IMDfreq 1
+# IMDwait -- wait for client to connect before starting simulation
+IMDwait on
+
+# IMD version -- 2 for VMD and 3 for latest protocol
+IMDversion 3
+# IMD session info settings
+# IMDsendPositions -- sending positions of entire system
+IMDsendPositions yes
+# IMDsendEnergies -- sending energies and bonded, non-bonded and other contributions
+IMDsendEnergies yes
+# IMDsendTime -- sending time information (time, dt, step)
+IMDsendTime yes
+# IMDsendBoxDimensions -- sending box dimensions (lattice vectors a, b, c)
+# If box dimensions are not defined, default unit box is sent
+IMDsendBoxDimensions yes
+# IMDsendVelocities -- sending velocities of entire system
+IMDsendVelocities yes
+# IMDsendForces -- sending forces on all atoms
+IMDsendForces yes
+# IMDwrapPositions -- wrapping positions to box; applicable when IMDsendPositions is yes
+IMDwrapPositions yes
diff --git a/examples/alanin/shorter-run/alanin.params b/examples/alanin/shorter-run/alanin.params
new file mode 100644
index 0000000..1690deb