Feature somd2

Hydration_freenrg/README.md

@@ -2,8 +2,12 @@
 A set of scripts used to reproduce the hydration free energy results of [Leoffler _et al_](10.1021/acs.jctc.8b00544) using BioSimSpace. Currently designed to be run specifically on the Yoko cluster.
 
 ## Usage
-* First run "run_generate.sh", this will generate smiles strings for all molecules in the "ligands" folder, placing a file named "SMILES.csv" in the "python" folder. It will then generate perturbable systems in both vacuum and solvent, reading the syste>
-* A folder named "Systems" will be created, containing all of the pertubable systems - this is where all simulation data will be stored. Currently 3 replicas of each system are generated.
-* One system generation is complete, run "MinEqallsystems.sh", this will loop over every perturbable system in "Systems", minimising the vacuum systems, and minimising and equilibrating the solvated systems.
-* Once Minimisation and equilibration are complete, run "runallsystems.sh". This will run all vacuum and solvated systems for all replicas (expect this to take a while).
-* Once all simulations are complete, run "analyse_all.sh" to analyse all simulations. This will generate a file called "Free_en_outs.out" in each perturbable system folder, as well as adding to the "results.csv" file in the "energy_results" folder.
+* First run ``run_generate.sh``, this will generate smiles strings for all molecules in the ``ligands`` folder, placing a file named ``SMILES.csv`` in the ``python`` folder. It will then generate perturbable systems in both vacuum and solvent.
+* A folder named ``Systems`` will be created, containing all of the pertubable systems - this is where all simulation data will be stored. Currently 3 replicas of each system are generated.
+* One system generation is complete, run ``min_eq_all_systems.sh``, this will loop over every perturbable system in ``Systems``, minimising the vacuum systems, and minimising and equilibrating the solvated systems. All minimisation and equilibration is perfromed using vanilla OpenMM.
+* Once Minimisation and equilibration are complete, simulations can be run using either ``SOMD1`` or ``SOMD2``. In order to run simulations using ``SOMD1`` run ``run_all_somd1.sh``. This will run all vacuum and solvated systems for all replicas using the SOMD1 protocol defined in ``mineq_solv.py`` and ``mineq_vac.py`` (expect this to take a while). In order to run simulations with ``SOMD2`` run ``run_all_somd2.sh``, this will run all vacuum and solvated legs using the protol defined in ``run_one_somd2.sh``.
+* Once all simulations are complete, run ``analyse_all_somd1.sh`` if SOMD1 was used to run simulations, or ``analyse_all_somd2`` if SOMD2 was used. This will generate a file called ``Free_en_outs.out`` in each perturbable system folder, as well as adding to the ``results.csv`` file in the ``energy_results`` folder.
+
+## Notes
+* Ensure that, prior to running scripts, the proper conda environment is listed in all bash scripts (``conda activate <your env name>``).
+* Protocols for SOMD1 and SOMD2 are defined differently: to alter SOMD1 protocols the relevant ``mineq_*.py`` script should be altered, to alter SOMD2 protocols, the ``run_one_somd2.sh`` script sohuld be altered.

Hydration_freenrg/bash_scripts/analyse_all.sh → Hydration_freenrg/bash_scripts/analyse_all_somd1.sh

@@ -22,7 +22,7 @@ for filename in ./Systems/*; do
         echo "System directory = $PWD"
 	systemfolder="$PWD"
 	for rep in ./rep*; do
-		cd $rep/solv
+		cd $rep/solvated_somd1
 		echo "$PWD"
 		cd lambda_0.0000
 		lj-tailcorrection -t somd.prm7 -c somd.rst7 -m somd.pert -C somd.cfg -l 0.00 -r traj000000001.dcd -s 1 1> ../freenrg-LJCOR-lam-0.000.dat 2> /dev/null
@@ -38,6 +38,6 @@ for filename in ./Systems/*; do
 	done
 	cd $maindir$filename
 	echo "HERE $PWD"
-	python $maindir/python/analysis.py > hydration_energy.out
+	python $maindir/python/analysis_somd1.py > hydration_energy.out
 	cd $maindir
 done

Hydration_freenrg/bash_scripts/analyse_all_somd2.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH -n 1
+#SBATCH --cpus-per-task 4
+    # allocate 5 GB of memory per job
+#SBATCH --mem 5000
+    # Set job name
+#SBATCH --job-name=analysis
+#SBATCH --output=./scriptouts/analysis.o
+#SBATCH --error=./scriptouts/analysis.err
+
+export CUDA_VISIBLE_DEVICES=""
+eval "$(conda shell.bash hook)"
+conda activate sireDEV
+python3 --version
+cd ../
+maindir="$PWD"
+echo "master dir is $maindir"
+for filename in "$maindir"/Systems/*; do
+        cd $filename
+        echo "System directory = $PWD"
+	systemfolder="$PWD"
+	cd $maindir$filename
+	echo "HERE $PWD"
+	python $maindir/python/analysis.py > hydration_energy.out
+	cd $maindir
+done
+

Hydration_freenrg/bash_scripts/min_eq_all_systems.sh

@@ -12,7 +12,7 @@
 #SBATCH --error=./scriptouts/MinEq.err
 
 eval "$(conda shell.bash hook)"
-conda activate openbiosim
+conda activate sireDEV
 python --version
 cd ../
 sdir="$PWD"

Hydration_freenrg/bash_scripts/min_eq_one_system.sh

@@ -14,7 +14,7 @@
 #Designed to be run from within the /Systems/{currentsystem} folder
 #Directory work should be handled by MinEqallsystems.sh
 eval "$(conda shell.bash hook)"
-conda activate openbiosim
+conda activate sireDEV
 python3 --version
 reps=( rep0 rep1 rep2 )
 rep=${reps[SLURM_ARRAY_TASK_ID]}

Hydration_freenrg/bash_scripts/run_all_systems.sh → Hydration_freenrg/bash_scripts/run_all_somd1.sh

@@ -12,7 +12,7 @@
 #SBATCH --error=./scriptouts/runall.err
 
 eval "$(conda shell.bash hook)"
-conda activate openbiosim
+conda activate sireDEV
 python3 --version
 cd ../
 maindir="$PWD"
@@ -22,8 +22,8 @@ for filename in ./Systems/*; do
 	for rep in ./rep*; do
 		cd $rep
 		echo "rep directory = $PWD"
-		sbatch --wait --array=0-16 $maindir/bash_scripts/run_one_system_solv.sh
-		sbatch --wait --array=0-16 $maindir/bash_scripts/run_one_system_vac.sh
+		sbatch --wait --array=0-16 $maindir/bash_scripts/run_one_solv_somd1.sh
+		sbatch --wait --array=0-16 $maindir/bash_scripts/run_one_vac_somd1.sh
 		cd ..
 	done
 	cd $maindir

Hydration_freenrg/bash_scripts/run_all_somd2.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+#SBATCH -n 1
+    # allocate 1 processor as a manager
+#SBATCH --cpus-per-task 1
+    # allocate 0.1 GB of memory per job
+#SBATCH --mem 100
+    # Set job name
+#SBATCH --job-name=runall
+#SBATCH --output=./scriptouts/runall_1fs.o
+#SBATCH --error=./scriptouts/runall_1fs.err
+
+eval "$(conda shell.bash hook)"
+conda activate sireDEV
+python3 --version
+cd ../
+maindir="$PWD"
+for filename in ./Systems/*; do
+        cd $filename
+        echo "System directory = $PWD"
+        for rep in ./rep*; do
+                cd $rep
+                echo "rep directory = $PWD"
+                sbatch --wait $maindir/bash_scripts/run_one_somd2.sh
+                cd ..
+        done
+        cd $maindir
+done
+

Hydration_freenrg/bash_scripts/run_generate.sh

@@ -12,7 +12,7 @@
 #SBATCH --error=./scriptouts/systemgenerate.err
 
 eval "$(conda shell.bash hook)"
-conda activate openbiosim
+conda activate sireDEV
 python3 --version
 ./convtoSMILES.sh
 cd ../

Hydration_freenrg/bash_scripts/run_one_system_solv.sh → Hydration_freenrg/bash_scripts/run_one_solv_somd1.sh

@@ -20,7 +20,7 @@ lam=${lamvals[SLURM_ARRAY_TASK_ID]}
 
 echo "lambda is: " $lam
 
-cd ./solv/lambda_$lam
+cd ./solvated_somd1/lambda_$lam
 echo "$PWD"
 srun somd-freenrg -C ./somd.cfg -c ./somd.rst7 -t ./somd.prm7 -m ./somd.pert -p CUDA -l $lam
 cd ..

Hydration_freenrg/bash_scripts/run_one_somd2.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+#SBATCH -n 1
+    # Request 1 gpu per job
+#SBATCH --gres=gpu:4
+    # allocate 5 processors/CPUs per GPU
+#SBATCH --cpus-per-gpu 4
+    # allocate 5 GB of memory per job
+#SBATCH --mem 5000
+    # Set job name
+#SBATCH --job-name=solv_run
+#SBATCH --output=run.%j.o
+#SBATCH --error=run.%j.er
+
+eval "$(conda shell.bash hook)"
+conda activate sireDEV
+python3 --version
+file_name_solv="mineq_solv.bss"
+file_name_vac="mineq_vac.bss"
+# Solvated leg
+somd2 ${file_name_solv} --runtime 500ps --timestep 1fs --h-mass-factor 1.0 --num-lambda 17 --temperature 298K --pressure 1atm --checkpoint-frequency 200ns --energy-frequency 0.25ps --output-directory solvated_somd2 --no-restart --cutoff-type rf --cutoff 10.0A --overwrite --perturbable-constraint none --constraint none --somd1-compatibility
+wait
+#Vacuum leg
+somd2 ${file_name_vac} --runtime 500ps --timestep 1fs --h-mass-factor 1.0 --num-lambda 17 --temperature 298K --checkpoint-frequency 1ns --output-directory vacuum_somd2 --energy-frequency 0.25ps --no-restart --cutoff-type rf --cutoff 10.0A --overwrite --perturbable-constraint none --constraint none --somd1-compatibility
+wait

Hydration_freenrg/bash_scripts/run_one_system_vac.sh → Hydration_freenrg/bash_scripts/run_one_vac_somd1.sh

@@ -20,7 +20,7 @@ lam=${lamvals[SLURM_ARRAY_TASK_ID]}
 
 echo "lambda is: " $lam
 
-cd ./vac/lambda_$lam
+cd ./vacuum_somd1/lambda_$lam
 echo "$PWD"
 srun somd-freenrg -C ./somd.cfg -c ./somd.rst7 -t ./somd.prm7 -m ./somd.pert -p CUDA -l $lam
 cd ..