adaptive data for tests

Acellera · Jun 17, 2024 · 63219f0 · 63219f0
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diff --git a/adaptivemd/data/e1s1_ntl9_1ns_0/output.xtc b/adaptivemd/data/e1s1_ntl9_1ns_0/output.xtc
diff --git a/adaptivemd/data/e1s2_ntl9_1ns_1/output.xtc b/adaptivemd/data/e1s2_ntl9_1ns_1/output.xtc
diff --git a/adaptivemd/data/e1s3_ntl9_1ns_2/output.xtc b/adaptivemd/data/e1s3_ntl9_1ns_2/output.xtc
diff --git a/adaptivemd/data/e2s1_e1s1p0f4/output.xtc b/adaptivemd/data/e2s1_e1s1p0f4/output.xtc
diff --git a/adaptivemd/data/e2s2_e1s2p0f3/output.xtc b/adaptivemd/data/e2s2_e1s2p0f3/output.xtc
diff --git a/adaptivemd/data/e3s1_e2s1p0f6/output.xtc b/adaptivemd/data/e3s1_e2s1p0f6/output.xtc
diff --git a/adaptivemd/data/e3s2_e1s1p0f1/output.xtc b/adaptivemd/data/e3s2_e1s1p0f1/output.xtc
diff --git a/adaptivemd/filtered/e1s1_ntl9_1ns_0/output.filtered.xtc b/adaptivemd/filtered/e1s1_ntl9_1ns_0/output.filtered.xtc
diff --git a/adaptivemd/filtered/e1s2_ntl9_1ns_1/output.filtered.xtc b/adaptivemd/filtered/e1s2_ntl9_1ns_1/output.filtered.xtc
diff --git a/adaptivemd/filtered/e1s3_ntl9_1ns_2/output.filtered.xtc b/adaptivemd/filtered/e1s3_ntl9_1ns_2/output.filtered.xtc
diff --git a/adaptivemd/filtered/e2s1_e1s1p0f4/output.filtered.xtc b/adaptivemd/filtered/e2s1_e1s1p0f4/output.filtered.xtc
diff --git a/adaptivemd/filtered/filtered.pdb b/adaptivemd/filtered/filtered.pdb
diff --git a/adaptivemd/filtered/filtered.psf b/adaptivemd/filtered/filtered.psf
diff --git a/adaptivemd/generators/ntl9_1ns_0/input b/adaptivemd/generators/ntl9_1ns_0/input
@@ -0,0 +1,18 @@
+bincoordinates                  input.coor
+coordinates                     structure.pdb
+cutoff                          9
+extendedsystem                  input.xsc
+thermostat                      on
+thermostatdamping               0.1
+thermostattemp                  350
+parameters                      parameters
+pme                             on
+restart                         on
+structure                       structure.psf
+switchdist                      7.5
+switching                       on
+temperature                     350
+timestep                        4
+trajectoryfile                  output.xtc
+trajectoryperiod                25000
+run                             250000 
diff --git a/adaptivemd/generators/ntl9_1ns_0/input.coor b/adaptivemd/generators/ntl9_1ns_0/input.coor
diff --git a/adaptivemd/generators/ntl9_1ns_0/input.xsc b/adaptivemd/generators/ntl9_1ns_0/input.xsc
@@ -0,0 +1,3 @@
+# Extended system configuration restart file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
+10000000 5.048889e+01 0 0 0 5.049091e+01 0 0 0 5.041617e+01 0 0 0 0 0 0 0 0 0
diff --git a/adaptivemd/generators/ntl9_1ns_0/parameters b/adaptivemd/generators/ntl9_1ns_0/parameters
diff --git a/adaptivemd/generators/ntl9_1ns_0/run.sh b/adaptivemd/generators/ntl9_1ns_0/run.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+acemd3 >log.txt 2>&1
+
diff --git a/adaptivemd/generators/ntl9_1ns_0/structure.pdb b/adaptivemd/generators/ntl9_1ns_0/structure.pdb
diff --git a/adaptivemd/generators/ntl9_1ns_0/structure.psf b/adaptivemd/generators/ntl9_1ns_0/structure.psf
diff --git a/adaptivemd/generators/ntl9_1ns_1/input b/adaptivemd/generators/ntl9_1ns_1/input
@@ -0,0 +1,18 @@
+bincoordinates                  input.coor
+coordinates                     structure.pdb
+cutoff                          9
+extendedsystem                  input.xsc
+thermostat                      on
+thermostatdamping               0.1
+thermostattemp                  350
+parameters                      parameters
+pme                             on
+restart                         on
+structure                       structure.psf
+switchdist                      7.5
+switching                       on
+temperature                     350
+timestep                        4
+trajectoryfile                  output.xtc
+trajectoryperiod                25000
+run                             250000 
diff --git a/adaptivemd/generators/ntl9_1ns_1/input.coor b/adaptivemd/generators/ntl9_1ns_1/input.coor
diff --git a/adaptivemd/generators/ntl9_1ns_1/input.xsc b/adaptivemd/generators/ntl9_1ns_1/input.xsc
@@ -0,0 +1,3 @@
+# Extended system configuration restart file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
+10000000 5.048889e+01 0 0 0 5.049091e+01 0 0 0 5.041617e+01 0 0 0 0 0 0 0 0 0
diff --git a/adaptivemd/generators/ntl9_1ns_1/parameters b/adaptivemd/generators/ntl9_1ns_1/parameters
diff --git a/adaptivemd/generators/ntl9_1ns_1/run.sh b/adaptivemd/generators/ntl9_1ns_1/run.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+acemd3 >log.txt 2>&1
+
diff --git a/adaptivemd/generators/ntl9_1ns_1/structure.pdb b/adaptivemd/generators/ntl9_1ns_1/structure.pdb
diff --git a/adaptivemd/generators/ntl9_1ns_1/structure.psf b/adaptivemd/generators/ntl9_1ns_1/structure.psf
diff --git a/adaptivemd/generators/ntl9_1ns_2/input b/adaptivemd/generators/ntl9_1ns_2/input
@@ -0,0 +1,18 @@
+bincoordinates                  input.coor
+coordinates                     structure.pdb
+cutoff                          9
+extendedsystem                  input.xsc
+thermostat                      on
+thermostatdamping               0.1
+thermostattemp                  350
+parameters                      parameters
+pme                             on
+restart                         on
+structure                       structure.psf
+switchdist                      7.5
+switching                       on
+temperature                     350
+timestep                        4
+trajectoryfile                  output.xtc
+trajectoryperiod                25000
+run                             250000 
diff --git a/adaptivemd/generators/ntl9_1ns_2/input.coor b/adaptivemd/generators/ntl9_1ns_2/input.coor
diff --git a/adaptivemd/generators/ntl9_1ns_2/input.xsc b/adaptivemd/generators/ntl9_1ns_2/input.xsc
@@ -0,0 +1,3 @@
+# Extended system configuration restart file
+#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
+10000000 5.048889e+01 0 0 0 5.049091e+01 0 0 0 5.041617e+01 0 0 0 0 0 0 0 0 0