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MD

MD simulations of lipid bilayers and photosensible molecules

Here I will try to put info of the status plot showing next:

This is the density of the last simulation

Procedure to obtain the CHARMM files

Ligand

  1. First we start the Ligand Reader & Modeler using the .mol2 file of the molecule.
  2. Select Make CGenFF topology, change the name and un-select Guess order
  3. Download the compressed file with the results, and check in the topology file LIG.rtf that the penalties are lower than 50.

Bilayer

  • Open PBD made by the ligand reader/modeler (ligandrm.pdb)
  • Use the original mol2 file(.rtf and .prm file in the residue folder: sometimes does not work)

Step1:

  • Check the structure
  • Align principal direction
  • Translate 50 A or 0 depending on out ir in the bilayer.

Step 2: Lipid components

  • Hidration number 50
  • Number of lipid components: 64 DOPC per leaflet
  • Show the system info button

Step 3:

  • Change to NaCl and delete KCl. Calculate solvetn composition

Next until

Step 5

  • GROMACS, NPT, 300K (Change)

Minimization

In the case that there is a problem during minimization using a single precision of GROMACS, please try to use a double precision of GROMACS only for the minimization step.

$ gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.0_minimization

Equilibration

$ gmx grompp -f step6.1_equilibration.mdp -o step6.1_equilibration.tpr -c step6.0_minimization.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.1_equilibration

$ gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -c step6.1_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.2_equilibration

$ gmx grompp -f step6.3_equilibration.mdp -o step6.3_equilibration.tpr -c step6.2_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.3_equilibration

$ gmx grompp -f step6.4_equilibration.mdp -o step6.4_equilibration.tpr -c step6.3_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.4_equilibration

$ gmx grompp -f step6.5_equilibration.mdp -o step6.5_equilibration.tpr -c step6.4_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.5_equilibration

$ gmx grompp -f step6.6_equilibration.mdp -o step6.6_equilibration.tpr -c step6.5_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step6.6_equilibration

Production

Before doing grompp, remember to change nsteps = 100000000, to set max time to 200ns.

$ gmx grompp -f step7_production.mdp -o step7_production.tpr -c step6.6_equilibration.gro -p topol.top -n index.ndx

$ gmx mdrun -v -deffnm step7_production -cpnum -ntmpi 1 -ntomp 16 -nsteps -1 -maxh 48 -cpt 60 -s step7_production.tpr

$ gmx mdrun -v -deffnm step7_production -cpnum -ntmpi 1 -ntomp 16 -nsteps -1 -maxh 48 -cpt 60 -s step7_production.tpr -cpi step7_production_stepXXX.cpt

TO run in OS-Carraixet gmx mdrun -v -deffnm step7_production -cpnum -nsteps -1 -maxh 48 -cpt 60 -s step7_production.tpr -cpi step7_production_stepXXX.cpt

For execution up to 200ns. `gmx mdrun -v -deffnm step7_production -cpnum -cpt 60 -s step7_production.tpr -cpi step7_production_stepXXX.cpt

Density

gmx density -s step7_production.tpr -f step7_production.trr -o density_OOPte_out_200ns.xvg -d Z -sl 500 -b 0 -e 20000000 -xvg none -ng 3 And then the order is, Water, DOPC and molecule

Trajectory

gmx trjconv -f step7.trr -s step7.tpr -o Ptr_out_100_200ns.pdb -b 100000 -e 200000 -skip 10000

gmx trjconv -f step7_inf.trr -s step7_new150ns.tpr -n index.ndx -o Memb_out_18000ps.pdb -dump 18000

gmx trjconv -f step7_inf.trr -s step7_new150ns.tpr -n index.ndx -o Odecyl_end_200_Ptr_out.pdb -b 190000 -e 200000

Change Production configuration

gmx grompp -f step7_production.mdp -c step7_new.tpr -o step7_new150ns.tpr -p topol.top -n index.ndx

Upload xvg data to repo

cp density_OCAP_in_200ns.xvg ../MD/script/last.xvg

cd ../MD/script/

nano last_data.dat

git pull

git add .

git commit -m 'OCAP 200ns in'

git push origin