Adding core gradient test1

tests/readme.md

@@ -6,13 +6,15 @@ Description of Q tests
 This ligand has pubchem cid 2203539:  
 <https://pubchem.ncbi.nlm.nih.gov/compound/2203539>
 
-And it's canonical SMILES is: 
+And its canonical SMILES is: 
 C1=CC(=CN=C1)CN2C(=O)C3=C(C2=O)C=C(C=C3)C(=O)NC4=CC(=CC(=C4)C(=O)O)C(=O)O
 
 
 ## Test 2 -- Same as test 1 but smoother ##
 
-This test is the same as in test 2, that is, the 2203539 ligand, but in this case a smoother equilibration protocol is used where heating, relaxation, and final equilibration steps are decoupled.
+This test is the  same as in test 2, that is,  the 2203539 ligand, but
+in this case a smoother  equilibration protocol is used where heating,
+relaxation, and final equilibration steps are decoupled.
 
 
 ## Test 3 -- A general FEP example ##
@@ -29,12 +31,18 @@ Here we try to reproduce the error.
 
 ## Test 5 -- DiHydroFolateReductase (DHFR) ##
 
-The CHARMM-AMBER benchmark molecule. DHFR has now become the standard benchmark for explicit solvent molecular dynamics in the majority of equations of motion solvers.
-As of March 2018 John Chodera from OpenMM claims that 506 ns/day are done in this test, and Ross Walker from AMBER claims 517.12 ns/day. The big difference is in the GPU cards they use. Chodera says the benchmark is using a GTX-1080Ti ($699 list price) and Ross Walker reports using a Titan V100 $8000.
+The CHARMM-AMBER benchmark molecule.  DHFR has now become the standard
+benchmark for  explicit solvent molecular dynamics in  the majority of
+equations  of motion  solvers.  As  of  March 2018  John Chodera  from
+OpenMM claims that  506 ns/day are done in this  test, and Ross Walker
+from  AMBER claims 517.12  ns/day. The  big difference  is in  the GPU
+cards they use. Chodera says the benchmark is using a GTX-1080Ti ($699
+list price) and Ross Walker reports using a Titan V100 $8000.
 
 
 ## Test 6 -- DNA and RNA using CHARMM36 ##
 
-Simple MD in Spherical Boundary Conditions to test the stability of DNA and RNA with respect to Arnott's fiber models.
+Simple MD  in Spherical Boundary  Conditions to test the  stability of
+DNA and RNA with respect to Arnott's fiber models.
 
 

tests/test1/README.md

@@ -2,8 +2,8 @@ Ligand in a water sphere test.
 ================================================================================
 
 This test follows an initial equilibration/heating protocol performed 
-in 5 steps and then a dynamics run split into 4 identical steps. A total of
-200ps are simulated after equilibration.
+in 5 steps and then a dynamics run split into 4 identical steps totalling
+160ps. A final "production run" of 200ps is run from file dc5.inp
 
 The system is a simple ligand in a water sphere and the
 force-field used is the OPLSAA force field from Jorgensen's lab.

tests/test1/nc12/benchmark.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#set -x
+#trap read debug
+
+#export rcran=/home/apps/R
+#export PATH=$rcran/bin:$PATH
+
+module load R/3.5.1-nsc1-gcc-2018a
+#module load buildenv-intel/2018b-eb
+#module load r/3.4.1
+
+echo "The following is the Q heating time in minutes: "
+    grep "Total time of main loop:" eq*.log | awk '{print $6}' | sed 's/(s)//g' \
+    | Rscript -e "A <- read.table(pipe('cat /dev/stdin')); (sum(A)/60)"
+
+echo "The following is the Q equilibration time in hours: "
+    grep "Total time of main loop:" dc*.log | awk '{print $6}' | sed 's/(s)//g' \
+    | Rscript -e "A <- read.table(pipe('cat /dev/stdin')); (sum(A)/60)/60"
+
+echo "The following is the Q heat+equilibration time in hours: "
+    grep "Total time of main loop:" *.log | awk '{print $6}' | sed 's/(s)//g' \
+    | Rscript -e "A <- read.table(pipe('cat /dev/stdin')); (sum(A)/60)/60"

tests/test1/nc12/dc1.inp

@@ -0,0 +1,38 @@
+[MD]
+steps                     20000
+stepsize                  2.0
+temperature               300.0
+bath_coupling             100
+random_seed               1
+initial_temperature       300.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                200
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   eq5.re
+final                     dc1.re
+trajectory                dc1.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/dc2.inp

@@ -0,0 +1,39 @@
+[MD]
+steps                     20000
+stepsize                  2.0
+temperature               300.0
+bath_coupling             100
+random_seed               1
+initial_temperature       300.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                200
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   dc1.re
+final                     dc2.re
+trajectory                dc2.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/dc3.inp

@@ -0,0 +1,38 @@
+[MD]
+steps                     20000
+stepsize                  2.0
+temperature               300.0
+bath_coupling             100
+random_seed               1
+initial_temperature       300.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                200
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   dc2.re
+final                     dc3.re
+trajectory                dc3.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/dc4.inp

@@ -0,0 +1,39 @@
+[MD]
+steps                     20000
+stepsize                  2.0
+temperature               300.0
+bath_coupling             100
+random_seed               1
+initial_temperature       300.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                200
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   dc3.re
+final                     dc4.re
+trajectory                dc4.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/dc5.inp

@@ -0,0 +1,39 @@
+[MD]
+steps                     100000
+stepsize                  2.0
+temperature               300.0
+bath_coupling             100
+random_seed               1
+initial_temperature       300.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                1000
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   dc4.re
+final                     dc5.re
+trajectory                dc5.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/eq1.inp

@@ -0,0 +1,37 @@
+[MD]
+steps                     100
+stepsize                  0.1
+initial_temperature       0.1
+temperature               0.1
+random_seed               1
+bath_coupling             1
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           off
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                1
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+final                     eq1.re
+trajectory                eq1.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1

tests/test1/nc12/eq2.inp

@@ -0,0 +1,39 @@
+[MD]
+steps                     1000
+stepsize                  2.0
+temperature               50.0
+bath_coupling             10
+random_seed               1
+initial_temperature       0.1
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                10
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   eq1.re
+final                     eq2.re
+trajectory                eq2.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1
+

tests/test1/nc12/eq3.inp

@@ -0,0 +1,39 @@
+[MD]
+steps                     1000
+stepsize                  2.0
+temperature               150.0
+bath_coupling             10
+random_seed               1
+initial_temperature       50.0
+shake_solvent             on
+shake_solute              off
+shake_hydrogens           on
+lrf                       on
+
+[cut_offs]
+solute_solute             10
+solute_solvent            10
+solvent_solvent           10
+q_atom                    99
+lrf                       99
+
+[sphere]
+shell_radius              16
+shell_force               20
+
+[intervals]
+non_bond                  25
+output                    50
+energy                    0
+trajectory                10
+
+[files]
+topology                  lig_w.top
+fep                       lig_w.fep
+restart                   eq2.re
+final                     eq3.re
+trajectory                eq3.dcd
+
+[sequence_restraints]
+1 46 0.5 0 1
+