imdclient 0.1.3__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (48) hide show
  1. imdclient/IMDClient.py +43 -12
  2. imdclient/IMDProtocol.py +1 -0
  3. imdclient/__init__.py +0 -5
  4. imdclient/data/gromacs/md/gromacs_v3_nst1.mdp +3 -3
  5. imdclient/data/namd/md/namd3 +0 -0
  6. imdclient/data/namd/md/namd_v3_nst_1.namd +1 -1
  7. imdclient/tests/base.py +108 -83
  8. imdclient/tests/conftest.py +0 -39
  9. imdclient/tests/datafiles.py +16 -1
  10. imdclient/tests/docker_testing/docker.md +1 -1
  11. imdclient/tests/hpc_testing/gromacs/README.md +112 -0
  12. imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp +58 -0
  13. imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.top +11764 -0
  14. imdclient/tests/hpc_testing/gromacs/struct.gro +21151 -0
  15. imdclient/tests/hpc_testing/gromacs/validate_gmx.sh +90 -0
  16. imdclient/tests/hpc_testing/lammps/README.md +62 -0
  17. imdclient/tests/hpc_testing/lammps/lammps_v3_nst_1.in +71 -0
  18. imdclient/tests/hpc_testing/lammps/topology_after_min.data +8022 -0
  19. imdclient/tests/hpc_testing/lammps/validate_lmp.sh +66 -0
  20. imdclient/tests/hpc_testing/namd/README.md +147 -0
  21. imdclient/tests/hpc_testing/namd/alanin.params +402 -0
  22. imdclient/tests/hpc_testing/namd/alanin.pdb +77 -0
  23. imdclient/tests/hpc_testing/namd/alanin.psf +206 -0
  24. imdclient/tests/hpc_testing/namd/namd_v3_nst_1.namd +59 -0
  25. imdclient/tests/hpc_testing/namd/validate_namd.sh +71 -0
  26. imdclient/tests/minimalreader.py +86 -0
  27. imdclient/tests/server.py +6 -14
  28. imdclient/tests/test_gromacs.py +15 -3
  29. imdclient/tests/test_imdclient.py +26 -7
  30. imdclient/tests/test_lammps.py +22 -19
  31. imdclient/tests/test_manual.py +224 -66
  32. imdclient/tests/test_namd.py +39 -16
  33. imdclient/tests/test_utils.py +31 -0
  34. imdclient/utils.py +50 -17
  35. {imdclient-0.1.3.dist-info → imdclient-0.2.0b0.dist-info}/METADATA +60 -39
  36. imdclient-0.2.0b0.dist-info/RECORD +53 -0
  37. {imdclient-0.1.3.dist-info → imdclient-0.2.0b0.dist-info}/WHEEL +1 -1
  38. {imdclient-0.1.3.dist-info → imdclient-0.2.0b0.dist-info/licenses}/AUTHORS.md +4 -1
  39. {imdclient-0.1.3.dist-info → imdclient-0.2.0b0.dist-info/licenses}/LICENSE +3 -1
  40. imdclient/IMD.py +0 -130
  41. imdclient/backends.py +0 -352
  42. imdclient/results.py +0 -332
  43. imdclient/streamanalysis.py +0 -1056
  44. imdclient/streambase.py +0 -199
  45. imdclient/tests/test_imdreader.py +0 -658
  46. imdclient/tests/test_stream_analysis.py +0 -61
  47. imdclient-0.1.3.dist-info/RECORD +0 -42
  48. {imdclient-0.1.3.dist-info → imdclient-0.2.0b0.dist-info}/top_level.txt +0 -0
imdclient/tests/hpc_testing/lammps/validate_lmp.sh ADDED
@@ -0,0 +1,66 @@
1
+ #!/bin/bash
2
+
3
+ # Default values
4
+ LAMMPS_BIN="lmp"
5
+ LAMMPS_INPUT="lammps_v3_nst_1.in"
6
+ TOPOL_PATH="topology_after_min.data"
7
+
8
+ OUTPUT_FILE="lammps_imd.out"
9
+ TRAJ_FILE="lammps_trj.h5md"
10
+
11
+ # Parse arguments
12
+ while [[ $# -gt 0 ]]; do
13
+ case $1 in
14
+ --lmp_bin)
15
+ LAMMPS_BIN="$2"
16
+ shift 2
17
+ ;;
18
+ --lmp_input)
19
+ LAMMPS_INPUT="$2"
20
+ shift 2
21
+ ;;
22
+ --topol_path)
23
+ TOPOL_PATH="$2"
24
+ shift 2
25
+ ;;
26
+ --mpi)
27
+ MPI=true
28
+ shift 1
29
+ ;;
30
+ *)
31
+ echo "Unknown argument: $1"
32
+ exit 1
33
+ ;;
34
+ esac
35
+ done
36
+
37
+ # Step 1: Run the LAMMPS simulation
38
+ echo "Starting LAMMPS simulation..."
39
+
40
+ if [ "$MPI" = true ]; then
41
+ echo "Running LAMMPS multi-node simulation with MPI & GPU support..."
42
+ mpiexec $LAMMPS_BIN -sf gpu -in $LAMMPS_INPUT &> $OUTPUT_FILE &
43
+ else
44
+ echo "Running LAMMPS single-node simulation..."
45
+ $LAMMPS_BIN -in $LAMMPS_INPUT &> $OUTPUT_FILE &
46
+ fi
47
+
48
+ # Wait for simulation to be ready
49
+
50
+ await_lmp_imd() {
51
+ grep -q "Waiting for IMD connection" "$OUTPUT_FILE"
52
+ }
53
+
54
+ while ! await_lmp_imd; do
55
+ echo "Waiting for LAMMPS IMD readiness in $OUTPUT_FILE..."
56
+ sleep 5
57
+ done
58
+
59
+ # Run test
60
+ echo "Running IMDClient manual test..."
61
+ python ../../test_manual.py \
62
+ --topol_path "$TOPOL_PATH" \
63
+ --traj_path "$TRAJ_FILE" \
64
+ --first_frame 1
65
+
66
+
imdclient/tests/hpc_testing/namd/README.md ADDED
@@ -0,0 +1,147 @@
1
+ # Manual validation of different compiler options for NAMD
2
+
3
+ ### Running tests
4
+
5
+ To validate all IMDv3 output (time, integration step, dt, box, positions, velocities, and forces)
6
+ against DCD output with a simple sample simulation, first ensure you're using a
7
+ python environment which has the testing requirements of IMDClient installed.
8
+
9
+ If not already installed, do:
10
+ ```bash
11
+ conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
12
+ conda activate imdclient-test
13
+ ```
14
+
15
+ Equivalently, on ASU's Sol, do:
16
+ ```bash
17
+ module load mamba
18
+ # Only needed for MPI builds
19
+ module load openmpi/4.1.5
20
+ conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
21
+ source activate imdclient-test
22
+ ```
23
+
24
+ Then, to run the test, do:
25
+ ```bash
26
+ cd imdclient/tests/hpc_testing/namd
27
+ chmod +x validate_namd.sh
28
+
29
+ ./validate_namd.sh \
30
+ --namd_binary /path/to/namd3
31
+ ```
32
+
33
+ To validate against your own simulation files, see `validate_namd.sh` for
34
+ command line arguments.
35
+
36
+ ### Compiling on ASU's Sol supercomputer
37
+
38
+ Allocate requisite resources (CPU cores, nodes, GPUs) on SOL and clone in https://gitlab.com/tcbgUIUC/namd.git
39
+
40
+ After cloning and `cd`-ing to `namd` folder if you're not already there, do:
41
+
42
+ ```bash
43
+ git checkout feature_imdv3
44
+ ```
45
+
46
+ Download and install TCL and FFTW libraries:
47
+ ```bash
48
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
49
+ tar xzf fftw-linux-x86_64.tar.gz
50
+ mv linux-x86_64 fftw
51
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64.tar.gz
52
+ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.6.13-linux-x86_64-threaded.tar.gz
53
+ tar xzf tcl8.6.13-linux-x86_64.tar.gz
54
+ tar xzf tcl8.6.13-linux-x86_64-threaded.tar.gz
55
+ mv tcl8.6.13-linux-x86_64 tcl
56
+ mv tcl8.6.13-linux-x86_64-threaded tcl-threaded
57
+ ```
58
+
59
+ Once can then download and unpack the Charm++ source code:
60
+
61
+ ```bash
62
+ wget https://github.com/charmplusplus/charm/archive/refs/tags/v8.0.0.tar.gz
63
+ tar xf v8.0.0.tar.gz
64
+ ```
65
+
66
+ Then, NAMD can be built with the following options:
67
+
68
+ #### Muticore version
69
+
70
+ ```bash
71
+ module load gcc-11.2.0-gcc-11.2.0
72
+
73
+ cd charm-8.0.0
74
+ ./build charm++ multicore-linux-x86_64 --with-production
75
+ cd ../../../../..
76
+
77
+ ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64
78
+
79
+ cd Linux-x86_64-g++
80
+ make
81
+ ```
82
+
83
+ #### InfiniBand UCX OpenMPI PMIx version
84
+
85
+ ```bash
86
+ module load gcc-11.2.0-gcc-11.2.0
87
+ module load openmpi/4.1.5
88
+ module load pmix/4.1.3-slurm
89
+
90
+ export CPATH="/packages/apps/pmix/4.1.3-slurm/include:$CPATH"
91
+ export LIBRARY_PATH="/packages/apps/pmix/4.1.3-slurm/lib:$LIBRARY_PATH"
92
+
93
+ cd charm-8.0.0
94
+ ./build charm++ ucx-linux-x86_64 ompipmix --with-production
95
+ cd ../../../../..
96
+
97
+ ./config Linux-x86_64-g++ --charm-arch ucx-linux-x86_64-ompipmix
98
+
99
+ cd Linux-x86_64-g++
100
+ make
101
+ ```
102
+
103
+ #### MPI version
104
+
105
+ ```bash
106
+ module load gcc-11.2.0-gcc-11.2.0
107
+ module load mpich/4.2.2
108
+
109
+ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
110
+ cd ../../../../..
111
+
112
+ ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
113
+
114
+ cd Linux-x86_64-g++
115
+ make
116
+ ```
117
+
118
+ #### GPU-resident CUDA multicore version
119
+
120
+ ```bash
121
+ module load gcc-11.2.0-gcc-11.2.0
122
+ module load mpich/4.2.2
123
+ module load cuda-11.8.0-gcc-11.2.0
124
+ module load gsl-2.7.1-gcc-11.2.0
125
+
126
+ cd charm-8.0.0
127
+ ./build charm++ multicore-linux-x86_64 --with-production
128
+ cd ../../../../..
129
+
130
+ ./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64 --with-single-node-cuda
131
+
132
+ cd Linux-x86_64-g++
133
+ make
134
+ ```
135
+
136
+ #### GPU-resident CUDA MPI version
137
+
138
+ ```bash
139
+ cd charm-8.0.0
140
+ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64-smp --with-production
141
+ cd
142
+
143
+ ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64-smp --with-single-node-cuda
144
+
145
+ cd Linux-x86_64-g++
146
+ make
147
+ ```
imdclient/tests/hpc_testing/namd/alanin.params ADDED
@@ -0,0 +1,402 @@
1
+ remark - parameter file PARAM19 -
2
+ remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
3
+ remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
4
+ remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
5
+
6
+ set echo=false end
7
+ !! - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974)
8
+ !! - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
9
+ !! - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1
10
+ !! The default h-bond exponents are now 6-repul 4-attr
11
+ !! ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++
12
+ !! Switched from Slater-Kirkwood to simple mixing rules - AB
13
+ !! Hbond parameters based on comparisons of dimer results with
14
+ !! ab initio calculations. - WER 12/19/84
15
+ !! Grouping of atom types for VDW parameters - BRB 1/3/85
16
+
17
+
18
+ bond C C 450.0 1.38! B. R. GELIN THESIS AMIDE AND DIPEPTIDES
19
+ bond C CH1E 405.0 1.52! EXCEPT WHERE NOTED. CH1E,CH2E,CH3E, AND CT
20
+ bond C CH2E 405.0 1.52! ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED
21
+ bond C CH3E 405.0 1.52
22
+ bond C CR1E 450.0 1.38
23
+ bond C CT 405.0 1.53
24
+ bond C N 471.0 1.33
25
+ bond C NC2 400.0 1.33! BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE
26
+ bond C NH1 471.0 1.33
27
+ bond C NH2 471.0 1.33
28
+ bond C NP 471.0 1.33
29
+ bond C NR 471.0 1.33
30
+ bond C O 580.0 1.23
31
+ bond C OC 580.0 1.23! FORCE DECREASE AND LENGTH INCREASE FROM C O
32
+ bond C OH1 450.0 1.38! FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
33
+ bond C OS 292.0 1.43! FROM DEP NORMAL MODE FIT
34
+ bond CH1E CH1E 225.0 1.53
35
+ bond CH1E CH2E 225.0 1.52
36
+ bond CH1E CH3E 225.0 1.52
37
+ bond CH1E N 422.0 1.45
38
+ bond CH1E NH1 422.0 1.45
39
+ bond CH1E NH2 422.0 1.45
40
+ bond CH1E NH3 422.0 1.45
41
+ bond CH1E OH1 400.0 1.42! FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
42
+ bond CH2E CH2E 225.0 1.52
43
+ bond CH2E CH3E 225.0 1.54
44
+ bond CH2E CR1E 250.0 1.45! FROM WARSHEL AND KARPLUS 1972 JACS 96:5612
45
+ bond CH2E N 422.0 1.45
46
+ bond CH2E NH1 422.0 1.45
47
+ bond CH2E NH2 422.0 1.45
48
+ bond CH2E NH3 422.0 1.45
49
+ bond CH2E OH1 400.0 1.42
50
+ bond CH2E S 450.0 1.81! FROM PARMFIX9
51
+ bond CH2E SH1E 450.0 1.81
52
+ bond CH3E NH1 422.0 1.49
53
+ bond CH3E NR 422.0 1.49 ! FOR NETROPSIN
54
+ bond CH3E S 450.0 1.77! FROM PARMFIX9
55
+ bond CH3E OS 292.0 1.38! FROM DEP NORMAL MODE FIT
56
+ bond CM OM 1115.0 1.128! FROM CAUGHEY ET AL(1978),CARBON MONOXIDE
57
+ bond CR1E CR1E 450.0 1.38
58
+ bond CR1E NH1 450.0 1.305
59
+ bond CR1E NR 450.0 1.305
60
+ bond CT CT 200.0 1.53
61
+ bond CT N 422.0 1.45
62
+ bond CT NC2 422.0 1.45
63
+ bond CT NH1 422.0 1.45
64
+ bond CT NH2 422.0 1.45
65
+ bond CT NH3 422.0 1.45
66
+ bond CT OH1 400.0 1.42
67
+ bond CT S 450.0 1.81
68
+ !bond FE CM 258.0 1.79! FROM KROEKER ET AL(JCP:72:4846)
69
+ !bond FE NP 500.0 2.09
70
+ !bond FE NR 65.0 1.98! FROM NAGAI ET AL(1980)
71
+ !bond FE OM 250.0 1.8! JUST A GUESS.
72
+ bond H NH1 405.0 0.98! GELIN AND IR STRETCH 3200 CM 1
73
+ bond H NH2 405.0 0.98
74
+ bond H OH1 450.0 0.96! FROM IR STRETCH 3400 CM 1
75
+ bond HA C 350.0 1.08
76
+ bond HA CT 300.0 1.08
77
+ bond HC NC2 405.0 1.00
78
+ bond HC NH1 405.0 0.98
79
+ bond HC NH3 405.0 1.04
80
+ bond OC S 400.0 1.43
81
+ bond OM OM 600.0 1.23! STRETCHING CONSTANT JUST A GUESS.
82
+ bond S S 500.0 2.02
83
+
84
+
85
+ angle C C C 70.0 106.5! FROM B. R. GELIN THESIS WITH HARMONIC
86
+ angle C C CH2E 65.0 126.5! PART OF F TERMS INCORPORATED. ATOMS
87
+ angle C C CH3E 65.0 126.5! WITH EXTENDED H COMPENSATED FOR LACK
88
+ angle C C CR1E 70.0 122.5! OF H ANGLES.
89
+ angle C C CT 70.0 126.5
90
+ angle C C HA 40.0 120.0! AMIDE PARAMETERS FIT BY LEAST SQUARES
91
+ angle C C NH1 65.0 109.0! TO N-METHYL ACETAMIDE VIBRATIONS.
92
+ angle C C NP 65.0 112.5! MINIMIZATION OF N-METHYL ACETAMIDE.
93
+ angle C C NR 65.0 112.5
94
+ angle C C OH1 65.0 119.0
95
+ angle C C O 65.0 119.0 ! FOR NETROPSIN
96
+ angle CH1E C N 20.0 117.5
97
+ angle CH1E C NH1 20.0 117.5
98
+ angle CH1E C O 85.0 121.5
99
+ angle CH1E C OC 85.0 117.5
100
+ angle CH1E C OH1 85.0 120.0
101
+ angle CH2E C CR1E 70.0 121.5
102
+ angle CH2E C N 20.0 117.5
103
+ angle CH2E C NH1 20.0 117.5
104
+ angle CH2E C NH2 20.0 117.5
105
+ angle CH2E C NC2 20.0 117.5 ! FOR NETROPSIN
106
+ angle CH2E C NR 60.0 116.0
107
+ angle CH2E C O 85.0 121.6
108
+ angle CH2E C OC 85.0 118.5
109
+ angle CH2E C OH1 85.0 120.0
110
+ angle CH3E C N 20.0 117.5
111
+ angle CH3E C NH1 20.0 117.5
112
+ angle CH3E C O 85.0 121.5
113
+ angle CR1E C CR1E 65.0 120.5
114
+ angle CR1E C NH1 65.0 110.5! USED ONLY IN HIS, NOT IT TRP
115
+ angle CR1E C NP 65.0 122.5
116
+ angle CR1E C NR 65.0 122.5
117
+ angle CR1E C OH1 65.0 119.0
118
+ angle CT C N 20.0 117.5
119
+ angle CT C NH1 20.0 117.5
120
+ angle CT C NH2 20.0 117.5
121
+ angle CT C O 85.0 121.5
122
+ angle CT C OC 85.0 118.5
123
+ angle CT C OH1 85.0 120.0
124
+ angle HA C NH1 40.0 120.0
125
+ angle HA C NH2 40.0 120.0
126
+ angle HA C NR 40.0 120.0
127
+ angle HA C O 85.0 121.5
128
+ angle N C O 85.0 121.0
129
+ angle NC2 C NC2 70.0 120.0
130
+ angle NC2 C NH1 70.0 120.0
131
+ angle NH1 C NR 70.0 120.0
132
+ angle NH1 C O 65.0 121.0
133
+ angle NH2 C O 65.0 121.0
134
+ angle O C OH1 85.0 120.0
135
+ angle OC C OC 85.0 122.5
136
+ angle OS C CH1E 70.0 125.3! FROM PARDNA10
137
+ angle OS C CH2E 70.0 125.3! - " -
138
+ angle OS C O 70.0 120.0! - " -
139
+ angle C CH1E CH1E 70.0 110.0
140
+ angle C CH1E CH2E 70.0 109.5
141
+ angle C CH1E CH3E 70.0 106.5
142
+ angle C CH1E N 45.0 111.6
143
+ angle C CH1E NH1 45.0 111.6
144
+ angle C CH1E NH2 45.0 111.6
145
+ angle C CH1E NH3 45.0 111.6
146
+ angle CH1E CH1E CH2E 45.0 112.5
147
+ angle CH1E CH1E CH3E 45.0 111.0
148
+ angle CH1E CH1E NH1 50.0 110.0
149
+ angle CH1E CH1E NH2 50.0 109.5
150
+ angle CH1E CH1E NH3 50.0 107.5
151
+ angle CH1E CH1E OH1 50.0 104.5
152
+ angle CH2E CH1E CH3E 50.0 111.5
153
+ angle CH2E CH1E N 65.0 104.0
154
+ angle CH2E CH1E NH1 65.0 110.0
155
+ angle CH2E CH1E NH2 65.0 110.0
156
+ angle CH2E CH1E NH3 65.0 110.0
157
+ angle CH3E CH1E CH3E 50.0 111.0
158
+ angle CH3E CH1E NH1 65.0 108.5
159
+ angle CH3E CH1E NH2 65.0 109.5
160
+ angle CH3E CH1E NH3 65.0 109.5
161
+ angle CH3E CH1E OH1 60.0 110.5
162
+ angle C CH2E CH1E 70.0 112.5
163
+ angle C CH2E CH2E 70.0 113.0
164
+ angle C CH2E NH1 70.0 111.6
165
+ angle C CH2E NH2 70.0 111.6
166
+ angle C CH2E NH3 70.0 111.6
167
+ angle CH1E CH2E CH1E 45.0 117.0
168
+ angle CH1E CH2E CH2E 45.0 112.5
169
+ angle CH1E CH2E CH3E 45.0 113.0
170
+ angle CH1E CH2E OH1 45.0 111.0
171
+ angle CH3E CH2E OH1 45.0 111.0
172
+ angle CH1E CH2E S 50.0 112.5
173
+ angle CH1E CH2E SH1E 50.0 112.5
174
+ angle CH2E CH2E CH2E 45.0 110.0
175
+ angle CH2E CH2E CH3E 45.0 111.0
176
+ angle CH2E CH2E N 65.0 105.0
177
+ angle CH2E CH2E NH1 65.0 111.0
178
+ angle CH2E CH2E NH2 65.0 109.5
179
+ angle CH2E CH2E NH3 65.0 110.5
180
+ angle CH2E CH2E S 50.0 112.5
181
+ angle C CR1E C 90.0 126.5
182
+ angle C CR1E CH2E 90.0 122.0
183
+ angle C CR1E CR1E 90.0 119.0
184
+ angle C CR1E NH1 90.0 109.5
185
+ angle C CR1E NR 90.0 106.5
186
+ angle CR1E CR1E CR1E 90.0 120.5
187
+ angle NH1 CR1E NH1 70.0 109.0
188
+ angle NH1 CR1E NR 70.0 109.0
189
+ angle C CT CT 70.0 109.5
190
+ angle C CT HA 70.0 109.5
191
+ angle C CT N 70.0 111.6
192
+ angle C CT NH1 70.0 111.6
193
+ angle C CT NH2 70.0 111.6
194
+ angle C CT NH3 70.0 111.6
195
+ angle CT CT CT 45.0 111.00
196
+ angle CT CT HA 40.0 109.50
197
+ angle CT CT N 65.0 105.00
198
+ angle CT CT NC2 65.0 110.00
199
+ angle CT CT NH1 65.0 110.00
200
+ angle CT CT NH2 65.0 110.00
201
+ angle CT CT NH3 65.0 110.00
202
+ angle CT CT OH1 50.0 109.50
203
+ angle CT CT S 50.0 112.50
204
+ angle HA CT HA 40.0 109.5
205
+ angle HA CT N 50.0 109.5
206
+ angle HA CT NC2 50.0 109.5
207
+ angle HA CT NH1 50.0 109.5
208
+ angle HA CT NH3 50.0 109.5
209
+ angle HA CT OH1 50.0 109.5
210
+ angle HA CT S 40.0 109.5
211
+ !angle FE CM OM 5.0 90.0! FROM KROEKER ET AL(1980)
212
+ angle C N CH1E 80.0 120.0
213
+ angle C N CH2E 80.0 120.0
214
+ angle C N CT 80.0 120.0
215
+ angle CH1E N CH2E 60.0 110.0
216
+ angle CH1E N CH3E 60.0 110.0
217
+ angle CH2E N CH3E 60.0 109.5
218
+ angle CT N CT 60.0 110.0
219
+ angle C NC2 CT 80.0 120.0
220
+ angle C NC2 HC 35.0 120.0
221
+ angle CT NC2 HC 35.0 120.0
222
+ angle HC NC2 HC 40.0 120.0
223
+ angle C NH1 C 60.0 102.5 ! UNUSED (AND PROBABLY WRONG)
224
+ angle C NH1 CH1E 77.5 120.0
225
+ angle C NH1 CH2E 77.5 120.0
226
+ angle C NH1 CH3E 77.5 120.0
227
+ angle C NH1 CR1E 60.0 108.0
228
+ angle C NH1 CT 80.0 120.0
229
+ angle C NH1 H 30.0 120.0
230
+ angle CH1E NH1 CH3E 60.0 120.0
231
+ angle CH1E NH1 H 35.0 120.0
232
+ angle CH2E NH1 CH3E 60.0 120.0
233
+ angle CH2E NH1 H 35.0 120.0
234
+ angle CH3E NH1 H 35.0 120.0
235
+ angle CR1E NH1 CR1E 65.0 110.0
236
+ angle CR1E NH1 H 35.0 120.0
237
+ angle CT NH1 H 35.0 120.0
238
+ angle C NH2 H 30.0 120.0
239
+ angle CH1E NH2 CH2E 60.0 120.0
240
+ angle CH1E NH2 H 35.0 120.0
241
+ angle CH2E NH2 H 35.0 120.0
242
+ angle CT NH2 H 35.0 120.0
243
+ angle H NH2 H 40.0 125.0
244
+ angle C NP C 70.0 102.5
245
+ !angle C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9
246
+ angle C NR C 70.0 102.5
247
+ angle C NR CR1E 70.0 109.5
248
+ angle CH3E NR CR1E 70.0 109.5 ! FOR NETROPSIN
249
+ angle CH3E NR C 70.0 109.5 ! FOR NETROPSIN
250
+ angle CR1E NR CR1E 65.0 110.0
251
+ !angle CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9
252
+ angle CH1E NH3 HC 35.0 109.5
253
+ angle CH1E NH3 CH2E 35.0 109.5
254
+ angle CH2E NH3 HC 35.0 109.5
255
+ angle CT NH3 HC 35.0 109.5
256
+ angle HC NH3 HC 40.0 109.5
257
+ angle C OH1 H 50.0 109.5
258
+ angle CH1E OH1 H 35.0 109.5
259
+ angle CH2E OH1 H 35.0 109.5
260
+ angle CT OH1 H 35.0 109.5
261
+ !angle FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS.
262
+ angle C OS CH3E 46.5 120.5! FROM PARDNA10
263
+ angle CH2E S CH3E 50.0 99.5! FROM PARMFIX9, CHECK WITH IR
264
+ angle CH2E S S 50.0 104.2
265
+ angle CT S CT 50.0 99.5! FORCE CONSTANTS FROM PARMFIX9
266
+ angle CT S S 50.0 104.2
267
+ angle OC S OC 85.0 109.5! FORCE CONSTANT JST A GUESS.
268
+ !angle NP FE CM 5.0 90.0
269
+ !angle NP FE NP 50.0 90.0
270
+ !angle NP FE NR 5.0 115.0
271
+ !angle NP FE OM 5.0 90.0! JUST A GUESS FROM EXISTING FE CM DATA
272
+ !angle NR FE CM 5.0 180.0
273
+ !angle NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA
274
+
275
+
276
+ dihe CH1E C N CH1E 10.0 2 180.0! PRO ISOM. BARRIER 20 KCAL/MOL.
277
+ dihe CH2E C N CH1E 10.0 2 180.0
278
+ dihe CR1E C C CR1E 5.0 2 180.0! => TRP OOP. VIB 170CM 1
279
+ dihe CR1E C C C 2.5 2 180.0! SEE BEHLEN ET AL JCP 75:5685 81
280
+ dihe CR1E C C NH1 2.5 2 180.0
281
+ dihe X C CH1E X 0.0 3 0.0! FROM GELIN THESIS AMIDES
282
+ dihe X C CH2E X 0.0 3 0.0! USING A SINGLE
283
+ dihe X C CR1E X 10.0 2 180.0! DIHEDRAL PER BOND RATHER
284
+ dihe X C CT X 0.0 3 0.0! THAN MULTIPLE TORSIONS.
285
+ dihe X C N X 8.2 2 180.0! ALKANE TORSION REDUCED TO
286
+ dihe X C NC2 X 8.2 2 180.0! 1.6 FROM 1.8 TO COINCIDE WITH
287
+ dihe X C NH1 X 8.2 2 180.0! THE EXPERIMENTAL BARRIER.
288
+ dihe X C NH2 X 8.2 2 180.0
289
+ dihe X C OH1 X 1.8 2 180.0
290
+ dihe X C OS X 1.8 2 180.0 ! INFERRED FROM C-OH1
291
+ dihe X CH1E CH1E X 1.6 3 0.0
292
+ dihe X CH1E CH2E X 1.6 3 0.0
293
+ dihe X CH1E N X 0.3 3 0.0! FROM HAGLER ET AL TABULATION OF
294
+ dihe X CH1E NH1 X 0.3 3 0.0! EXP. DATA AND 6 31G CALC.
295
+ dihe X CH1E NH2 X 1.8 3 0.0! PROTONATED SECONDARY AMINE
296
+ dihe X CH1E NH3 X 0.6 3 0.0! 1/PROTON SO 3 FOR THE BOND
297
+ dihe X CH1E OH1 X 0.5 3 0.0! CHANGED TO ROUGHLY MEOH
298
+ dihe X CH2E CH2E X 1.6 3 0.0
299
+ dihe X CH2E N X 0.3 3 0.0! SEE CH1E COMMENTS
300
+ dihe X CH2E NH1 X 0.3 3 0.0
301
+ dihe X CH2E NH2 X 0.6 3 0.0
302
+ dihe X CH2E NH3 X 0.6 3 0.0
303
+ dihe X CH2E OH1 X 0.5 3 0.0
304
+ dihe X CH2E S X 1.2 2 0.0
305
+ dihe X CT CT X 1.6 3 0.0
306
+ dihe X CT N X 0.3 3 0.0! SEE CH1E COMMENTS
307
+ dihe X CT NC2 X 0.3 3 0.0
308
+ dihe X CT NH1 X 0.3 3 0.0
309
+ dihe X CT NH2 X 0.6 3 0.0
310
+ dihe X CT NH3 X 0.6 3 0.0
311
+ dihe X CT OH1 X 0.5 3 0.0
312
+ dihe X CT S X 1.2 2 0.0
313
+ !dihe X FE NR X 0.05 4 0.0
314
+ !dihe X FE CM X 0.05 4 0.0
315
+ !dihe X FE OM X 0.00 4 0.0
316
+ dihe X S S X 4.0 2 0.0! FROM EXP.R BARRI
317
+
318
+
319
+ impr C C CR1E CH2E 90.0 0 0.0!GIVE 220 CM 1 METHYL OOP FOR TOLUENE.
320
+ impr C CR1E C CH2E 90.0 0 0.0!USED HERE FOR TRP CG OUT OF PLANE
321
+ impr C CR1E CR1E CH2E 90.0 0 0.0! PHE, AND TYR CG OOP
322
+ impr C CR1E NH1 CH2E 90.0 0 0.0! HIS CG RING OOP
323
+ impr C NH1 CR1E CH2E 90.0 0 0.0!
324
+ impr C CR1E CR1E OH1 150.0 0 0.0! GIVE 249 CM 1 PHENOL OH OOP.
325
+ impr C H H NH2 45.0 0 0.0! PRIMARY AMIDES (ASN AND GLN) OOP
326
+ impr C OC OC CH1E 100.0 0 0.0! CARBOXYL OUT OF PLANE.
327
+ impr C OC OC CH2E 100.0 0 0.0!
328
+ impr C X X C 25.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS
329
+ impr C X X CH2E 90.0 0 0.0! FROM TOLUENE METHYL OOP. 217 CM 1
330
+ impr C X X CH3E 90.0 0 0.0
331
+ impr C X X CR1E 25.0 0 0.0
332
+ impr C X X H 75.0 0 0.0! FROM BENZENE NORMAL MODE ANALYSIS
333
+ impr C X X HA 75.0 0 0.0!
334
+ impr C X X NH1 100.0 0 0.0! AMIDES FIT TO N METHYL ACETAMIDE.
335
+ impr C X X O 100.0 0 0.0
336
+ impr C X X OC 100.0 0 0.0
337
+ impr C X X OH1 150.0 0 0.0! USED FOR TYR HYDROXYL OOP
338
+ impr CH1E X X CH1E 55.0 0 35.26439! CALCULATED TO BE THE SAME AS THE 3
339
+ impr CH1E X X CH2E 55.0 0 35.26439! H CH1E X ANGLES WITH K=40
340
+ impr CH1E X X CH3E 55.0 0 35.26439
341
+ impr CR1E X X CR1E 25.0 0 0.0! EXTENDED ATOM VERSION OF BENZENE
342
+ impr CR1E X X NH1 25.0 0 0.0! SAME AS ABOVE FOR LACK OF VALUES
343
+ !impr FE X X NP 20.0 0 0.0! FROM PARMFIX9
344
+ impr H X X O 45.0 0 0.0
345
+ impr N CH1E CH2E C 45.0 0 0.0! PROLINE NITROGENS
346
+ impr N X X CH2E 45.0 0 0.0
347
+ impr N X X CT 45.0 0 0.0
348
+ impr NC2 X X CT 45.0 0 0.0
349
+ impr NC2 X X HC 45.0 0 0.0
350
+ impr NH1 X X CH1E 45.0 0 0.0
351
+ impr NH1 X X CH2E 45.0 0 0.0
352
+ impr NH1 X X CH3E 45.0 0 0.0
353
+ impr NH1 X X CT 45.0 0 0.0
354
+ impr NH1 X X H 45.0 0 0.0! AMIDES PROTON OOP
355
+ impr NH1 X X NH1 25.0 0 0.0!
356
+ impr NH1 X X NR 25.0 0 0.0
357
+ impr NH2 X X H 45.0 0 0.0
358
+ impr NR X X C 25.0 0 0.0
359
+ impr NR X X CR1E 25.0 0 0.0
360
+ impr NR X X CT 25.0 0 0.0
361
+ impr NR X X CH3E 25.0 0 0.0 ! FOR NETROPSIN
362
+
363
+
364
+
365
+ {* nonbonding parameter section *}
366
+ {* ============================ *}
367
+
368
+ ! eps sigma eps(1:4) sigma(1:4)
369
+ ! (kcal/mol) (A)
370
+ ! ---------------------------------------
371
+ NONBonded H 0.0498 1.4254 0.0498 1.4254
372
+ NONBonded HA 0.0450 2.6157 0.0450 2.6157 !- charged group.
373
+ NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius
374
+ !
375
+ NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon
376
+ NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \
377
+ NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons
378
+ NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! /
379
+ !! NONBonded CM 0.0262 4.4367 0.1000 3.3854
380
+ NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons
381
+ !! NONBonded CT 0.0262 4.4367 0.1000 3.3854
382
+ !
383
+ NONBonded N 0.2384 2.8509 0.2384 2.8509
384
+ NONBonded NC2 0.2384 2.8509 0.2384 2.8509
385
+ NONBonded NH1 0.2384 2.8509 0.2384 2.8509
386
+ NONBonded NH2 0.2384 2.8509 0.2384 2.8509
387
+ NONBonded NH3 0.2384 2.8509 0.2384 2.8509
388
+ NONBonded NP 0.2384 2.8509 0.2384 2.8509
389
+ NONBonded NR 0.2384 2.8509 0.2384 2.8509
390
+ !
391
+ NONBonded O 0.1591 2.8509 0.1591 2.8509
392
+ NONBonded OC 0.6469 2.8509 0.6469 2.8509
393
+ NONBonded OH1 0.1591 2.8509 0.1591 2.8509
394
+ !! NONBonded OM 0.1591 2.8509 0.1591 2.8509
395
+ NONBonded OS 0.1591 2.8509 0.1591 2.8509
396
+ !
397
+ NONBonded S 0.0430 3.3676 0.0430 3.3676
398
+ NONBonded SH1E 0.0430 3.3676 0.0430 3.3676
399
+ !
400
+ !! NONBONDED FE 0.0000 1.1582 0.0000 1.1582
401
+
402
+ set echo=true end
imdclient/tests/hpc_testing/namd/alanin.pdb ADDED
@@ -0,0 +1,77 @@
1
+ REMARK FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PDB"
2
+ REMARK PARAM11.PRO ( from PARAM6A )
3
+ REMARK ===========
4
+ REMARK PROTEIN PARAMETERS:
5
+ REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
6
+ REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
7
+ REMARK LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4
8
+ REMARK CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.
9
+ REMARK JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
10
+ REMARK DATE:16-Feb-89 11:21:32 created by user: nonella
11
+ ATOM 1 CA ACE 1 -2.184 0.591 0.910 0.0 10.0 MAIN
12
+ ATOM 2 C ACE 1 -0.665 0.627 0.966 100.0 0.0 MAIN
13
+ ATOM 3 O ACE 1 -0.069 1.213 1.868 100.0 0.0 MAIN
14
+ ATOM 4 N ALA 2 0.000 0.000 0.000 100.0 0.0 MAIN
15
+ ATOM 5 H ALA 2 -0.490 -0.462 -0.712 100.0 0.0 MAIN
16
+ ATOM 6 CA ALA 2 1.450 0.000 0.000 0.0 10.0 MAIN
17
+ ATOM 7 CB ALA 2 1.969 -0.670 -1.262 100.0 0.0 MAIN
18
+ ATOM 8 C ALA 2 2.010 1.413 0.000 100.0 0.0 MAIN
19
+ ATOM 9 O ALA 2 2.911 1.748 0.767 100.0 0.0 MAIN
20
+ ATOM 10 N ALA 3 1.488 2.280 -0.863 100.0 0.0 MAIN
21
+ ATOM 11 H ALA 3 0.770 1.998 -1.467 100.0 0.0 MAIN
22
+ ATOM 12 CA ALA 3 1.981 3.643 -0.909 0.0 10.0 MAIN
23
+ ATOM 13 CB ALA 3 1.147 4.464 -1.880 100.0 0.0 MAIN
24
+ ATOM 14 C ALA 3 1.865 4.326 0.444 100.0 0.0 MAIN
25
+ ATOM 15 O ALA 3 2.801 4.963 0.924 100.0 0.0 MAIN
26
+ ATOM 16 N ALA 4 0.710 4.211 1.093 100.0 0.0 MAIN
27
+ ATOM 17 H ALA 4 -0.026 3.700 0.697 100.0 0.0 MAIN
28
+ ATOM 18 CA ALA 4 0.541 4.841 2.388 0.0 10.0 MAIN
29
+ ATOM 19 CB ALA 4 -0.809 4.462 2.976 100.0 0.0 MAIN
30
+ ATOM 20 C ALA 4 1.591 4.371 3.381 100.0 0.0 MAIN
31
+ ATOM 21 O ALA 4 2.212 5.167 4.085 100.0 0.0 MAIN
32
+ ATOM 22 N ALA 5 1.818 3.063 3.463 100.0 0.0 MAIN
33
+ ATOM 23 H ALA 5 1.315 2.443 2.895 100.0 0.0 MAIN
34
+ ATOM 24 CA ALA 5 2.809 2.556 4.392 0.0 10.0 MAIN
35
+ ATOM 25 CB ALA 5 2.970 1.055 4.209 100.0 0.0 MAIN
36
+ ATOM 26 C ALA 5 4.176 3.170 4.142 100.0 0.0 MAIN
37
+ ATOM 27 O ALA 5 4.859 3.615 5.064 100.0 0.0 MAIN
38
+ ATOM 28 N ALA 6 4.611 3.212 2.886 100.0 0.0 MAIN
39
+ ATOM 29 H ALA 6 4.055 2.853 2.163 100.0 0.0 MAIN
40
+ ATOM 30 CA ALA 6 5.908 3.786 2.586 0.0 10.0 MAIN
41
+ ATOM 31 CB ALA 6 6.121 3.830 1.082 100.0 0.0 MAIN
42
+ ATOM 32 C ALA 6 6.012 5.221 3.079 100.0 0.0 MAIN
43
+ ATOM 33 O ALA 6 6.992 5.614 3.710 100.0 0.0 MAIN
44
+ ATOM 34 N ALA 7 5.002 6.040 2.802 100.0 0.0 MAIN
45
+ ATOM 35 H ALA 7 4.228 5.711 2.297 100.0 0.0 MAIN
46
+ ATOM 36 CA ALA 7 5.044 7.419 3.245 0.0 10.0 MAIN
47
+ ATOM 37 CB ALA 7 3.730 8.110 2.918 100.0 0.0 MAIN
48
+ ATOM 38 C ALA 7 5.219 7.518 4.752 100.0 0.0 MAIN
49
+ ATOM 39 O ALA 7 6.045 8.278 5.255 100.0 0.0 MAIN
50
+ ATOM 40 N ALA 8 4.445 6.748 5.512 100.0 0.0 MAIN
51
+ ATOM 41 H ALA 8 3.792 6.148 5.096 100.0 0.0 MAIN
52
+ ATOM 42 CA ALA 8 4.566 6.799 6.956 0.0 10.0 MAIN
53
+ ATOM 43 CB ALA 8 3.670 5.747 7.589 100.0 0.0 MAIN
54
+ ATOM 44 C ALA 8 5.984 6.488 7.409 100.0 0.0 MAIN
55
+ ATOM 45 O ALA 8 6.560 7.186 8.241 100.0 0.0 MAIN
56
+ ATOM 46 N ALA 9 6.582 5.429 6.871 100.0 0.0 MAIN
57
+ ATOM 47 H ALA 9 6.109 4.882 6.209 100.0 0.0 MAIN
58
+ ATOM 48 CA ALA 9 7.934 5.082 7.264 0.0 10.0 MAIN
59
+ ATOM 49 CB ALA 9 8.436 3.918 6.425 100.0 0.0 MAIN
60
+ ATOM 50 C ALA 9 8.898 6.233 7.027 100.0 0.0 MAIN
61
+ ATOM 51 O ALA 9 9.705 6.584 7.887 100.0 0.0 MAIN
62
+ ATOM 52 N ALA 10 8.839 6.851 5.851 100.0 0.0 MAIN
63
+ ATOM 53 H ALA 10 8.190 6.560 5.176 100.0 0.0 MAIN
64
+ ATOM 54 CA ALA 10 9.733 7.956 5.567 0.0 10.0 MAIN
65
+ ATOM 55 CB ALA 10 9.388 8.570 4.219 100.0 0.0 MAIN
66
+ ATOM 56 C ALA 10 9.595 9.067 6.595 100.0 0.0 MAIN
67
+ ATOM 57 O ALA 10 10.580 9.587 7.117 100.0 0.0 MAIN
68
+ ATOM 58 N ALA 11 8.364 9.460 6.912 100.0 0.0 MAIN
69
+ ATOM 59 H ALA 11 7.590 9.036 6.488 100.0 0.0 MAIN
70
+ ATOM 60 CA ALA 11 8.169 10.516 7.887 0.0 10.0 MAIN
71
+ ATOM 61 CB ALA 11 6.686 10.695 8.168 100.0 0.0 MAIN
72
+ ATOM 62 C ALA 11 8.823 10.177 9.217 100.0 0.0 MAIN
73
+ ATOM 63 O ALA 11 9.523 10.992 9.815 100.0 0.0 MAIN
74
+ ATOM 64 N CBX 12 8.610 8.962 9.714 100.0 0.0 MAIN
75
+ ATOM 65 H CBX 12 8.050 8.324 9.225 100.0 0.0 MAIN
76
+ ATOM 66 CA CBX 12 9.223 8.571 11.014 0.0 10.0 MAIN
77
+ END