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SimpleMembranes/1.BuildCOBY.sh

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+pip install COBY
+
+# DOPC-CHOL membrane 
+python -m COBY -box 20 20 20 -membrane lipid:DOPC:7 lipid:CHOL:3 -solvation default -sn DOPC_CHOL
+
+# DOPE-DOPG membrane
+python -m COBY -box 20 20 20 -membrane lipid:DOPE:7 lipid:DOPG:3 -solvation default -sn DOPE_DOPG
+
+# General command
+# python -m COBY -box x y x -membrane lipid:lipidtype:lipidratio -solvation solv:solventype pos:posion neg:negion -sn systemname
+
+# Default box type is rectangular but can set hexagonal, skewed hexagonal and rhombic dodecahedron or manually designate the unit cell
+# Default solvation corresponds to 0.15 M NaCl + any additional ions to counter charged lipid heads
+# By default the command will output a .gro , .pdb and .top file 
+
+# For additional commands and extra information refer to https://github.com/MikkelDA/COBY
+# Specifically https://doi.org/10.1101/2024.07.23.604601 , https://github.com/MikkelDA/COBY/blob/master/COBY_Documentation.pdf and https://github.com/MikkelDA/COBY/blob/master/COBY_CHEAT_SHEET.pdf

SimpleMembranes/2.GenerateIndex.sh

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+systemname=""
+
+# Will create an index file defining which particles belong to the 'Solvent' and 'Membrane' groups
+# Useful for simulation conditions where system components need to be treated with separate conditions e.g. temp or pressure
+
+echo "keep 0" > index-selection.txt
+echo "r W | r NA | r CL" >> index-selection.txt
+echo "name 1 Solvent" >> index-selection.txt
+echo '!1' >> index-selection.txt
+echo "name 2 Membrane" >> index-selection.txt
+echo "q" >> index-selection.txt
+
+gmx make_ndx -f ${systemname}.gro -o index.ndx < index-selection.txt

SimpleMembranes/3.TopologyFix.sh

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+systemname=""
+
+cp ITPs.txt temp
+grep -v "include" ${systemname}.top >> temp
+mv temp ${systemname}.top
+
+# Will append all necessary topology definitions to the COBY generated .top file

SimpleMembranes/4.EquilibrationRuns.sh

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+
+systemname=""
+
+# Energy minimisation using the steepest descent algorithm - 1500 steps
+
+gmx grompp -c ${systemname}.gro -r ${systemname}.gro -f minimisation.mdp -p ${systemname}.top -o em.tpr -maxwarn 5
+gmx mdrun -s em.tpr -deffnm em 
+
+# Time step: 1 fs , Total time: 5 ps , Thermostat: Berendsen , Barostat: Berendsen (τP = 10 ps)
+
+gmx grompp -c em.gro -r em.gro -f equilibration1.mdp -p ${systemname}.top -o eq1.tpr -maxwarn 5 -n index.ndx
+gmx mdrun -s eq1.tpr -deffnm eq1 
+
+# Time step: 5 fs , Total time: 100 ps , Thermostat: Berendsen , Barostat: Berendsen (τP = 3 ps)
+
+gmx grompp -c eq1.gro -r em.gro -f equilibration2.mdp -p ${systemname}.top -o eq2.tpr -maxwarn 5 -n index.ndx
+gmx mdrun -s eq2.tpr -deffnm eq2  
+
+# Time step: 10 fs , Total time: 400 ps , Thermostat: Berendsen , Barostat: Berendsen (τP = 3 ps)
+
+gmx grompp -c eq2.gro -r em.gro -f equilibration3.mdp -p ${systemname}.top -o eq3.tpr -maxwarn 5 -n index.ndx
+gmx mdrun -s eq3.tpr -deffnm eq3  
+
+# Time step: 20 fs , Total time: 2 ns , Thermostat: v-rescale , Barostat: c-rescale (τP = 4 ps) 
+
+gmx grompp -c eq3.gro -r em.gro -f preproduction.mdp -p ${systemname}.top -o preproduction.tpr -maxwarn 5 -n index.ndx 
+gmx mdrun -s preproduction.tpr -deffnm preproduction  
+
+# Time step: 20 fs , Total time: 2 µs , Thermostat: v-rescale , Barostat: c-rescale (τP = 4 ps) - production run will vary in timescale depending on lipid mixture 
+
+gmx grompp -c preproduction.gro -r em.gro -f production.mdp -p ${systemname}.top -o production.tpr -maxwarn 5 -n index.ndx
+gmx mdrun -s production.tpr -deffnm production 
+
+# All commands and .mdp files have been downloaded/modified from https://doi.org/10.1016/bs.mie.2024.03.010 and https://bbs.llnl.gov/building_membranes_data.html - refer to for further information

SimpleMembranes/ITPs.txt

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+#include "/path/m3.0.0/martini_v3.0.0.itp"
+#include "/path/m3.0.0/martini_v3.0.0_phospholipids_v1.itp"
+#include "/path/m3.0.0/martini_v3.0_sterols_v1.0.itp"
+#include "/path/m3.0.0/martini_v3.0.0_solvents_v1.itp"  
+#include "/path/m3.0.0/martini_v3.0.0_ions_v1.itp"  

SimpleMembranes/equilibration1.mdp

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+;
+; STANDARD MD INPUT OPTIONS FOR MARTINI 3 ALPHA
+;
+define                   = -DPOS_Z_RES 
+integrator               = md
+dt                       = 0.001
+nsteps                   = 5000
+nstcomm                  = 100
+comm-grps		 = System
+
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 25000
+nstenergy                = 25000
+nstxout-compressed       = 25000
+compressed-x-precision   = 100
+compressed-x-grps        =
+energygrps               = System
+
+
+; NEIGHBOURLIST and MARTINI
+; See Kim et al. 2023 (10.26434/chemrxiv-2023-zbj6j) and de Jong et al. 2016 (10.1016/j.cpc.2015.09.014)
+cutoff-scheme            = Verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz 
+verlet-buffer-tolerance  = -1
+nsttcouple               = 20 
+nstpcouple               = 20
+rlist                    = 1.35
+
+coulombtype              = reaction-field
+rcoulomb                 = 1.1
+epsilon_r                = 15
+epsilon_rf               = 0
+vdw_type                 = cutoff
+vdw-modifier             = Potential-shift-verlet
+rvdw                     = 1.1
+
+; MARTINI and TEMPERATURE/PRESSURE
+tcoupl                   = berendsen
+tc-grps                  = Solvent Membrane
+tau_t                    = 1.0 1.0
+ref_t                    = 310 310
+Pcoupl                   = berendsen
+Pcoupltype               = semiisotropic
+tau_p                    = 10.0
+compressibility          = 3e-4 3e-4
+ref_p                    = 1.0  1.0
+refcoord-scaling         = all
+
+gen_vel                  = yes
+gen_temp                 = 310
+gen_seed                 = 4722423
+
+constraints              = none
+constraint_algorithm     = Lincs
+lincs_order              = 8
+lincs_warnangle          = 90
+lincs_iter               = 2

SimpleMembranes/equilibration2.mdp

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+;
+; STANDARD MD INPUT OPTIONS FOR MARTINI 3 ALPHA
+;
+define                   = -DPOS_Z_RES
+integrator               = md
+dt                       = 0.005
+nsteps                   = 20000
+nstcomm                  = 100
+comm-grps		 = System
+
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 25000
+nstenergy                = 25000
+nstxout-compressed       = 25000
+compressed-x-precision   = 100
+compressed-x-grps        =
+energygrps               = System
+
+
+; NEIGHBOURLIST and MARTINI
+; See Kim et al. 2023 (10.26434/chemrxiv-2023-zbj6j) and de Jong et al. 2016 (10.1016/j.cpc.2015.09.014)
+cutoff-scheme            = Verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+verlet-buffer-tolerance  = -1
+nsttcouple               = 20
+nstpcouple               = 20
+rlist                    = 1.35
+
+coulombtype              = reaction-field
+rcoulomb                 = 1.1
+epsilon_r                = 15
+epsilon_rf               = 0
+vdw_type                 = cutoff
+vdw-modifier             = Potential-shift-verlet
+rvdw                     = 1.1
+
+tcoupl                   = berendsen
+tc-grps                  = Solvent Membrane
+tau_t                    = 1.0 1.0
+ref_t                    = 310 310
+Pcoupl                   = berendsen
+Pcoupltype               = semiisotropic
+tau_p                    = 3.0
+compressibility          = 3e-4  3e-4
+ref_p                    = 1.0  1.0
+refcoord-scaling         = all
+
+gen_vel                  = no
+gen_temp                 = 310
+gen_seed                 = 472229
+
+constraints              = none
+constraint_algorithm     = Lincs
+lincs_order              = 8
+lincs_warnangle          = 90
+lincs_iter               = 2

SimpleMembranes/equilibration3.mdp

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+;
+; STANDARD MD INPUT OPTIONS FOR MARTINI 3 ALPHA
+;
+define                   = -DPOS_Z_RES
+integrator               = md
+dt                       = 0.01
+nsteps                   = 40000
+nstcomm                  = 100
+comm-grps		 = System
+
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 25000
+nstenergy                = 25000
+nstxout-compressed       = 25000
+compressed-x-precision   = 100
+compressed-x-grps        =
+energygrps               = System
+
+; NEIGHBOURLIST and MARTINI
+; See Kim et al. 2023 (10.26434/chemrxiv-2023-zbj6j) and de Jong et al. 2016 (10.1016/j.cpc.2015.09.014)
+cutoff-scheme            = Verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+verlet-buffer-tolerance  = -1
+nsttcouple               = 20
+nstpcouple               = 20
+rlist                    = 1.35
+
+coulombtype              = reaction-field
+rcoulomb                 = 1.1
+epsilon_r                = 15
+epsilon_rf               = 0
+vdw_type                 = cutoff
+vdw-modifier             = Potential-shift-verlet
+rvdw                     = 1.1
+
+tcoupl                   = berendsen
+tc-grps                  = Solvent Membrane
+tau_t                    = 1.0 1.0
+ref_t                    = 310 310
+Pcoupl                   = berendsen
+Pcoupltype               = semiisotropic
+tau_p                    = 3.0
+compressibility          = 3e-4  3e-4
+ref_p                    = 1.0  1.0
+refcoord_scaling         = all
+
+gen_vel                  = no
+gen_temp                 = 310
+gen_seed                 = 473529
+
+constraints              = none
+constraint_algorithm     = Lincs
+lincs_order              = 8
+lincs_warnangle          = 90
+lincs_iter               = 2

SimpleMembranes/minimisation.mdp

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+;
+; STANDARD MD INPUT OPTIONS FOR MARTINI 3 ALPHA
+;
+define                   = -DPOS_Z_RES 
+integrator               = steep
+nsteps                   = 1500
+nstcomm                  = 100
+comm-grps		 =
+
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 1000
+nstenergy                = 100
+nstxout-compressed       = 1000
+compressed-x-precision   = 100
+compressed-x-grps        =
+energygrps               =
+
+; NEIGHBOURLIST and MARTINI
+; See Kim et al. 2023 (10.26434/chemrxiv-2023-zbj6j) and de Jong et al. 2016 (10.1016/j.cpc.2015.09.014)
+
+cutoff-scheme            = Verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+verlet-buffer-tolerance  = 0.005
+
+coulombtype              = reaction-field
+rcoulomb                 = 1.1
+epsilon_r                = 15
+epsilon_rf               = 0
+vdw_type                 = cutoff
+vdw-modifier             = Potential-shift-verlet
+rvdw                     = 1.1
+
+constraints              = none
+constraint_algorithm     = Lincs
+lincs-order              = 8
+lincs-iter               = 2
+lincs-warnangle          = 90

SimpleMembranes/preproduction.mdp

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+;
+; STANDARD MD INPUT OPTIONS FOR MARTINI 3 ALPHA
+;
+define                   = -DPOS_Z_RES
+integrator               = md
+dt                       = 0.02
+nsteps                   = 100000
+
+nstxout                  = 0
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 25000
+nstenergy                = 25000
+nstxout-compressed       = 25000
+compressed-x-precision   = 100
+compressed-x-grps        =
+energygrps               = System
+
+; NEIGHBOURLIST and MARTINI
+; See Kim et al. 2023 (10.26434/chemrxiv-2023-zbj6j) and de Jong et al. 2016 (10.1016/j.cpc.2015.09.014)
+cutoff-scheme            = Verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+verlet-buffer-tolerance  = -1
+nsttcouple               = 20
+nstpcouple               = 20
+rlist                    = 1.35
+
+coulombtype              = reaction-field
+rcoulomb                 = 1.1
+epsilon_r                = 15
+epsilon_rf               = 0
+vdw_type                 = cutoff
+vdw-modifier             = Potential-shift-verlet
+rvdw                     = 1.1
+
+;Temperature coupling
+tcoupl                   = v-rescale
+tc-grps                  = Solvent Membrane
+tau_t                    = 1.0 1.0
+ref_t                    = 310 310
+
+; Pressure coupling     
+Pcoupl                   = c-rescale
+Pcoupltype               = semiisotropic
+tau_p                    = 4.0 
+ref_p                    = 1.0 1.0
+compressibility          = 3e-4 3e-4 
+
+; Center of mass removal
+comm-mode                = Linear
+nstcomm                  = 100
+comm-grps                = Solvent Membrane
+
+refcoord_scaling         = all ;not-needed when no restraints applied
+
+gen_vel                  = no
+gen_temp                 = 310
+gen_seed                 = 474429
+
+constraints              = none
+constraint_algorithm     = Lincs
+lincs_order              = 8
+lincs_warnangle          = 90
+lincs_iter               = 2